Category: Population Genetics

French Canadians are genetically special (not that that’s a good thing)

By Razib Khan | September 30, 2013 2:40 am

Jack Kerouac, credit: Tom Palumbo

The Pith: Higher Mendelian disease rates among French Canadians may be due to their demographic history.

As I have noted before, demographic bottlenecks with extremely strong effects on the character of population genetic variation need to be very radical in their nature to be of any significance. The population pinhole has to be on the order of hundreds, rather than thousands, of individuals. But that does not preclude more modest bottlenecks generating subtle shifts in the genetic site frequency spectrum. Strong bottlenecks may be needed to drive wholesale extinction of once common alleles (or the fixation of those at moderate frequencies), but mild bottlenecks may nevertheless perturb the allele frequency distribution. In particular, the number of alleles which are present at very low frequencies can be strongly impacted by demographic variation and natural selection. This is the logical rationale which serves as the basis for nucleotide sequence based tests for detecting natural selection, such as Tajima’s D. An excess of low frequency variants suggest a bottleneck and subsequent population expansion, or positive and/or purifying selection. In contrast, balanced polymorphism frequencies point to a shrinking population or balancing selection.

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CATEGORIZED UNDER: Population Genetics

Buddy, can you spare a genetic distance statistic?

By Razib Khan | July 20, 2013 4:13 am

Sewall Wright
Credit: University of Wisconsin, Madison

You have probably heard or read that most genetic variation is within races, not between races. This assertion has led, in my opinion, to unwarranted inferences. Often bracketed under “Lewontin’s Fallacy”, the basic intuition is that if most variation is within races, then races as a taxonomic unit are without utility or substantive basis. This is disputable. In plain English, though most genetic variation may be within races (i.e., not diagnostic of racial identity), the variation across races is quite systematic because that variation reflects deep population history. In this way of thinking population or racial substructure are simply reflections of the tips of the tree which has been shaped by history.

But these discussions are ultimately predicated upon a statistic, FST. FST is generally considered one of the fixation indices pioneered by the American evolutionary geneticist Sewall Wright. What Wright’s FST aims to capture is the relative amount of genetic variance which is due population substructure. In regards to human races out of the total genetic variation ~15% of it can be inferred simply by looking at population substructure (FST ~0.15), with the balance not being due to population structure. But this is an average value. At rs1426654 in SLC24A5 when comparing Europeans and Africans almost all of the variation is between the populations, because the allele frequencies are disjoint. But what if I told you that Wright’s FST is quite a bit woollier than you might think?

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CATEGORIZED UNDER: Population Genetics
MORE ABOUT: Fst, Genetic Distance

Population genetics on the cheap!

By Razib Khan | June 12, 2013 9:35 am

Textbooks are often very expensive. For example the most recent edition of Principles of Population Genetics will run you $50-$100. But it has come to my attention that the third edition of this textbook is potentially much cheaper, with some copies in the <$10 range! Population genetics isn’t quite like math, where 19th century works are still interesting to the non-specialist (population genetics was ‘invented’ in the first decades of the 20th century!). But a lot of the older material is totally relevant and on point, so these previous editions are not just simply historical curiosities. Much of the third and fourth editions of this particular work overlap anyhow, the big difference obviously being genomic techniques and such. But for that you should probably read papers, many of which are thankfully being put out as preprints now.

While I’m at it, I notice there are some affordable copies ($10-$20) of Genetics of Human Populations. This is a very old work from decades ago. But it is an encyclopedic treatment of the post-World War II human genetic literature, much of which has been forgotten or faded, but perhaps should not be discarded so lightly….

Update: I realize on second thought that it was remiss of me to not point out that Graham Coop and Joe Felsenstein both have free population genetics resources which readers might find highly useful. Also see these notes from U Conn.

CATEGORIZED UNDER: Population Genetics

Vulcans through the eye of the bottleneck

By Razib Khan | May 20, 2013 3:44 am

The Black Death

I noticed during Peter Ralph and Graham Coop’s Ask Me Anything about their new paper, The Geography of Recent Genetic Ancestry across Europe, someone brought up the effects of plague. Recall that ~1/3 of Europe’s population died during the Black Death. And population size reductions on the order of ~50% due to epidemics are not unknown in human history. Surely this would have a major genetic effect? Well, in fact it would have a genetic effect due to possible adaptations to disease (see CCR5). But there would be little overall impact on genetic diversity, at least in the short term. That is because for bottlenecks to produce major change in the genetic character of a population they have to be rather extreme in magnitude.

This issue came to mind for me in 2009 when I watched Stark Trek. If you haven’t watched the J. J. Abrams reboot, and are a spoilerphobe, read no more! Now, with that out of the way you may recall that during this film the Vulcans suffered a genocidal attack. Out of billions of Vulcans only ~10,000 survived. Here’s some commentary on the possible consequences, New Star Trek Movie: A Vulcan Holocaust?:

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Revisiting the architecture of evolution

By Razib Khan | March 5, 2013 3:43 am

Baroque?

An old argument going back to the origins of theoretical population genetics has to do with the nature of the genetic effects which control traits and are subject to change in allele frequency due to adaptation. Often these are bracketed as part of the controversies between R. A. Fisher and Sewall Wright (see Sewall Wright and Evolutionary Biology). In short, Fisher contended that most evolution through adaptation was driven by selection operating upon additive genetic variation. That is, variation due to alleles across the genome, each having independent and additive effects on the trait. One might think of these as linear effects. In contrast Wright’s views were more complex or confused, depending upon your perspective on the sum totality of his theories. In the domain of genetic architecture he presented a model where gene-gene interactions, epistasis, played an important role in the evolutionary trajectory of populations, which traversed ‘adaptive landscapes’ in a contingent fashion.

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CATEGORIZED UNDER: Population Genetics

Using your 23andMe data: how inbred are you?

By Razib Khan | January 9, 2013 1:24 am

Earlier editions:

Using your 23andMe data: exploring with MDS
Using your 23andMe data in Plink

From Reconstructing Indian Population History:

We hypothesize that founder effects are responsible for an even higher burden of recessive diseases in India than consanguinity. To test this hypothesis, we used our data to estimate the probability that two alleles from a group share a common ancestor more recently than that group’s divergence from other Indians, and compared this to the probability that an individual’s two alleles share an ancestor in the last few generations due to consanguinity…Nine of the 15 Indian groups for which we could make this assessment had a higher probability of recessive disease due to founder events than to consanguinity, including all the Indo-European speaking groups (Table 2). It is important to systematically survey Indian groups to identify those with the strongest founder effects, and to prioritize them for studies to identify recessive diseases and map genes.

South Asian populations exhibit a lot of between population genetic distance, and not simply as a function of geography. With more markers and an expansive data set Dan MacArthur will be able to assess exactly which South Asian caste his ancestry is from.

But this is an issue where I have fancied myself an outlier. My own background is moderately heterogeneous, and I’ve always explained to people that I’m not inbred like most South Asians, only half in jest (from what I can tell Muslims in the subcontinent have castes too, though they may somewhat different terminology). I know that my paternal grandmother came from a Brahmin family (clear by the customs preserved in the family even in her generation), while my maternal grandfather was almost certainly from a group with a Kayastha origin (going by surname, and who my mother actually clusters with). My maternal grandmother had considerable non-Bengali ancestry, which does show up in Middle Eastern signatures in my mother.

But this is talk. Am I truly not as inbred as the average brown? Leveraging methods which I discussed earlier (see posts above) I can very quickly check this.

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MORE ABOUT: 23andMe, Inbreeding, PLINK

Unveiling the genealogical lattice

By Razib Khan | December 18, 2012 3:01 am

To understand nature in all its complexity we have to cut down the riotous variety down to size. For ease of comprehension we formalize with math, verbalize with analogies, and visualize with representations. These approximations of reality are not reality, but when we look through the glass darkly they give us filaments of essential insight. Dalton’s model of the atom is false in important details (e.g., fundamental particles turn out to be divisible into quarks), but it still has conceptual utility.

Likewise, the phylogenetic trees popularized by L. L. Cavalli-Sforza in The History and Geography of Human Genes are still useful in understanding the shape of the human demographic past. But it seems that the bifurcating model of the tree must now be strongly tinted by the shades of reticulation. In a stylized sense inter-specific phylogenies, which assume the approximate truth of the biological species concept (i.e., little gene flow across lineages), mislead us when we think of the phylogeny of species on the microevolutionary scale of population genetics. On an intra-specific scale gene flow is not just a nuisance parameter in the model, it is an essential phenomenon which must be accommodated into the framework.

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Is Daniel MacArthur ‘desi’?

By Razib Khan | December 10, 2012 4:07 am

My initial inclination in this post was to discuss a recent ordering snafu which resulted in many of my friends being quite peeved at 23andMe. But browsing through their new ‘ancestry composition’ feature I thought I had to discuss it first, because of some nerd-level intrigue. Though I agree with many of Dienekes concerns about this new feature, I have to admit that at least this method doesn’t give out positively misleading results. For example, I had complained earlier that ‘ancestry painting’ gave literally crazy results when they weren’t trivial. It said I was ~60 percent European, which makes some coherent sense in their non-optimal reference population set, but then stated that my daughter was >90 percent European. Since 23andMe did confirm she was 50% identical by descent with me these results didn’t make sense; some readers suggested that there was a strong bias in their algorithms to assign ambiguous genomic segments to ‘European’ heritage (this was a problem for East Africans too).

Here’s my daughter’s new chromosome painting:

One aspect of 23andMe’s new ancestry composition feature is that it is very Eurocentric. But, most of the customers are white, and presumably the reference populations they used (which are from customers) are also white. Though there are plenty of public domain non-white data sets they could have used, I assume they’d prefer to eat their own data dog-food in this case. But that’s really a minor gripe in the grand scheme of things. This is a huge upgrade from what came before. Now, it’s not telling me, as a South Asian, very much. But, it’s not telling me ludicrous things anymore either!

But in regards to omission I am curious to know why this new feature rates my family as only ~3% East Asian, when other analyses put us in the 10-15% range. The problem with very high values is that South Asians often have some residual ‘eastern’ signal, which I suspect is not real admixture, but is an artifact. Nevertheless, northeast Indians, including Bengalis, often have genuine East Asia admixture. On PCA plots my family is shifted considerably toward East Asians. The signal they are picking up probably isn’t noise. Almost every apportionment of East Asian ancestry I’ve seen for my family yields a greater value for my mother, and that holds here. It’s just that the values are implausibly low.

In any case, that’s not the strangest thing I saw. I was clicking around people who I had “shared” genomes with, and I stumbled upon this:

As you can guess from the screenshot this is Daniel MacArthur’s profile. And according to this ~25% of chromosome 10 is South Asian! On first blush this seemed totally nonsensical to me, so I clicked around other profiles of people of similar Northern European background…and I didn’t see anything equivalent.

What to do? It’s going to take more evidence than this to shake my prior assumptions, so I downloaded Dr. MacArthur’s genotype. Then I merged it with three HapMap populations, the Utah whites (CEU), the Gujaratis (GIH), and the Chinese from Denver (CHD). The last was basically a control. I pulled out chromosome 10. I also added Dan’s wife Ilana to the data set, since I believe she got typed with the same Illumina chip, and is of similar ethnic background (i.e., very white). It is important to note that only 28,000 SNPs remained in the data set. But usually 10,000 is more than sufficient on SNP data for model-based clustering with inter-continental scale variation.

I did two things:

1) I ran ADMIXTURE at K = 3, unsupervised

2) I ran an MDS, which visualized the genetic variation in multiple dimensions

Before I go on, I will state what I found: these methods supported the inference from 23andMe, on chromosome 10 Dr. MacArthur seems to have an affinity with South Asians (i.e., this is his ‘curry chromosome’). Here are the average (median) values in tabular format, with MacArthur and his wife presented for comparison.

ADMIXTURE results for chromosome 10
K 1 K 2 K 3
CEU 0.04 0.02 0.93
GIH 0.87 0.05 0.08
CHD 0.01 0.97 0.01
Daniel MacArthur 0.29 0.07 0.64
Ilana Fisher 0.01 0.06 0.94

You probably want a distribution. Out of the non-founder CEU sample none went above 20% South Asian. Though it did surprise me that a few were that high, making it more plausible to me that MacArthur’s results on chromosome 10 were a fluke:

And here’s the MDS with the two largest dimensions:

Again, it’s evident that this chromosome 10 is shifted toward South Asians. If I had more time right now what I’d do is probably get that specific chromosomal segment, phase it, and then compare it to various South Asian populations. But I don’t have time now, so I went and checked out the results from the Interpretome. I cranked up the settings to reduce the noise, and so that it would only spit out the most robust and significant results. As you can see, again chromosome 10 comes up as the one which isn’t quite like the others.

Is there is a plausible explanation for this? Perhaps Dr. MacArthur can call up a helpful relative? From what  recall his parents are immigrants from the United Kingdom, and it isn’t unheard of that white Britons do have South Asian ancestry which dates back to the 19th century. Though to be totally honest I’m rather agnostic about all this right now. This genotype has been “out” for years now, so how is it that no one has noticed this peculiarity??? Perhaps the issue is that everyone was looking at the genome wide average, and it just doesn’t rise to the level of notice? What I really want to do is look at the distribution of all chromosomes and see how Daniel MacArthur’s chromosome 10 then stacks up. It might be a random act of nature yet.

Also, I guess I should add that at ~1.5% South Asian that would be consistent with one of MacArthur’s great-great-great-great grandparents being Indian. Assuming 25 year generation times that puts them in the mid-19th century. Of course, at such a low proportion the variance is going to be high, so it is quite possible that you need to push the real date of admixture one generation back, or one generation forward.

Northern Europeans and Native Americans are not more closely related than previously thought

By Razib Khan | December 1, 2012 3:38 pm

A new press release is circulating on the paper which I blogged a few months ago, Ancient Admixture in Human History. Unlike the paper, the title of the press release is misleading, and unfortunately I notice that people are circulating it, and probably misunderstanding what is going on. Here’s the title and first paragraph:

Native Americans and Northern Europeans More Closely Related Than Previously Thought

Released: 11/30/2012 2:00 PM EST
Source: Genetics Society of America

Newswise — BETHESDA, MD – November 30, 2012 — Using genetic analyses, scientists have discovered that Northern European populations—including British, Scandinavians, French, and some Eastern Europeans—descend from a mixture of two very different ancestral populations, and one of these populations is related to Native Americans. This discovery helps fill gaps in scientific understanding of both Native American and Northern European ancestry, while providing an explanation for some genetic similarities among what would otherwise seem to be very divergent groups. This research was published in the November 2012 issue of the Genetics Society of America’s journal GENETICS

 

The reality is ta Native Americans and Northern Europeans are not more “closely related” genetically than they were before this paper. There has been no great change to standard genetic distance measures or phylogeographic understanding of human genetic variation. A measure of relatedness is to a great extent a summary of historical and genealogical processes, and as such it collapses a great deal of disparate elements together into one description. What the paper in Genetics outlined was the excavation of specific historically contingent processes which result in the summaries of relatedness which we are presented with, whether they be principal component analysis, Fst, or model-based clustering.

What I’m getting at can be easily illustrated by a concrete example. To the left is a 23andMe chromosome 1 “ancestry painting” of two individuals. On the left is me, and the right is a friend. The orange represents “Asian ancestry,” and the blue represents “European” ancestry. We are both ~50% of both ancestral components. This is a correct summary of our ancestry, as far as it goes. But you need some more information. My friend has a Chinese father and a European mother. In contrast, I am South Asian, and the end product of an ancient admixture event. You can’t tell that from a simple recitation of ancestral quanta. But it is clear when you look at the distribution of ancestry on the chromosomes. My components have been mixed and matched by recombination, because there have been many generations between the original admixture and myself. In contrast, my friend has not had any recombination events between his ancestral components, because he is the first generation of that combination.

So what the paper publicized in the press release does is present methods to reconstruct exactly how patterns of relatedness came to be, rather than reiterating well understood patterns of relatedness. With the rise of whole-genome sequencing and more powerful computational resources to reconstruct genealogies we’ll be seeing much more of this to come in the future, so it is important that people are not misled as to the details of the implications.

A plea for population genetics

By Razib Khan | October 10, 2012 10:31 pm

The title here is somewhat misleading. This is not just a plea for population genetics, but for quantitative genetics as well. Genetics is a big field. But today it is defined by and large by DNA, the concrete entity in which the abstraction of the gene is embedded. Look at the header of this website, or the background to my Twitter account. Mind you, I’m pathetically informed about molecular genetics, and don’t have a strong interest in the topic! I did consider using the H.W.E. or the breeder’s equation for the header, but in the end I judged it too abstruse and unfamiliar to most readers. DNA dominates when it comes to the modern mental conception of genetics, and we have to live with it to some extent.
But there is also great value in the genetics which has intellectual roots in the pre-DNA Mendelians and biometricians. This genetics exhibits a symbiotic, but not necessary, association with genetics as a branch of biophysics. Yet I come here not to insult or impugn my friends who toil in the trenches of the molecular wars. Rather, I simply want to point out that our world needs balance, and the systematic aerial perspective of population, evolutionary, and quantitative genetics can provide a different kind of intellectual ballast. More importantly, for the mnemonically lazy in the audience pop, evo, and quant gives you information for free. By this, I mean that these are highly theoretical fields, and theory can predict and allow you to infer facts about the world. You don’t need immerse yourself in every scrap of data if you can derive the likely probable pattern from theory.


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CATEGORIZED UNDER: Population Genetics

What is inbreeding?

By Razib Khan | July 22, 2012 10:23 pm

I’ve put up a bunch of posts relating to inbreeding recently (1, 2, 3, 4). But I haven’t really defined it. First, let’s stipulate what inbreeding is not: it is not the same as incest. Acts of incest can include individuals who have no blood relationship to each other (e.g., Hamlet). Additionally, there are instances of inbreeding which are not necessarily incestuous. If a population is highly inbred, then individuals who are not relations by social custom may still be so genetically similar to a point where the pairing can not credibly be stated as an outcross. But still, what do I mean? To refresh myself I re-read the section on inbreeding in Hartl & Clark. And I think that helped clarify one implicit assumption which I have which may not be clear to everyone, and I’ll get to that.

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CATEGORIZED UNDER: Population Genetics
MORE ABOUT: Inbreeding

On theoretical evolutionary genetics

By Razib Khan | July 1, 2012 11:13 pm

Joe Felsenstein in the comments:

The books you have listed are good ones, by fine people. But may I immodestly suggest a book of mine? If you want to work your way through the theory of theoretical population genetics, I have set of notes for my Genome 562 course, a textbook. It is a freely-downloadable PDF (start with my website by clicking on my name in this comment). It’s not for everyone but I think those interested in knowing how the theory actually works in more detail will benefit from it. As it’s free, I have no monetary interest in calling your attention to it, just pure ego. (And if you want a one-locus population genetics simulation program, try PopG at my lab’s website too — Google “Felsenstein PopG”).

Many of the books I recommended below are rather expensive. Theoretical Evolutionary Genetics (PDF) is not. Unfortunately much of the discourse of contemporary science is beyond the financial means of much of the world’s population, whether it be in university press textbooks or gated journals. So I’m quite happy in putting up a link to this text-in-progress.

CATEGORIZED UNDER: Population Genetics

Learning population and evolutionary genetics

By Razib Khan | July 1, 2012 12:44 pm

A reader emailed me to ask what I thought would be a good way to better understand some of the more technical posts I put up.

First, two course notes which I’ve found useful as personal references:

EEB 5348 — Population Genetics

Evolutionary Quantitative Genetics, Uppsala University (if you are ambitious, bookmark this too)

Some people might argue that John Gillespie’s Population Genetics: A Concise Guide (Kindle edition) is a touch too abstruse and cryptic for the introductory reader. It’s short, and the mathematics isn’t challenging, but because of its concision the author can sometimes unleash upon your nearly cryptic formalism, perhaps defeating the purpose of a soft introduction in the first place. To get the most out of this book you probably ironically have to have a more thorough textbook on hand to clear up those particular points which you find confusing. But to get the general logic of population genetics and establish familiarity this seems to be the right entry point (assuming you’re not to terrified by algebra).

Of course most readers of this weblog are focused more particularly on the topic of evolution, and evolutionary genetics. Evolutionary Genetics by the late great John Maynard Smith is a rather good full-spectrum introduction into this topic. It covers many of the topics in the Gillespie book, though less mathematically intensively. But this is not not just a population genetics books, and expands into other topics of relevance to evolutionary genetics (e.g., of course phylogenetics gets a big shout out). And Smith has richer empirical examples too. This is probably a less intimidating book than Population Genetics, but I’d recommend you hit it second because it will make much more sense if you’ve got some of the foundations undernearth you.


Some of you though might be a little on the unbalanced side. I actually “learned” population genetics (if it can be said I know population genetics, I’d more honestly state I’d familiar with population genetics) through Principles of Population Genetics, the “Hartl & Clark” book. This is not really an introductory book, but I think in some ways it’s more comprehensible than Population Genetics, because it doesn’t need to be concise. Sometimes formal methods in pop gen only make sense with lots of empirical examples and worked out problems, and this is a book which has the scope in terms of space for that. There’s really no big downside I can give for getting this book. I’ve got he 2nd, 3rd, and 4th editions, mostly because I couldn’t find an affordable copy of the 3rd in the early 2000s, while the 4th came out literally right after I purchased the 3rd!

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CATEGORIZED UNDER: Population Genetics

Where the wild clines aren't

By Razib Khan | March 7, 2012 7:38 pm

In the recent ‘do human races’ exist controversy Nick Matzke’s post Continuous geographic structure is real, “discrete races” aren’t has become something of a touchstone (perhaps a post like Cosma Shalizi’s on I.Q. and heritability).* In the post Matzke emphasized the idea of clines, roughly a continuous gradient of genetic change over space. Fair enough. But in the map above I traced two linear transects. I would suggest that anyone who has a general understanding of the demographics of South-Central Eurasia would immediately anticipate that these transects would reveal a relatively sharp break in allele frequencies. True, there are intermediate populations between the two end points, in Nepal, and on the fringes of India’s northeastern states. But clearly about halfway through the southwest-northeast transect you’ll see a rapid shift in allele frequencies. The blue transect is different, insofar as the change occurs very near its eastern pole. In Bengal, 85% of the length of the transect from its western terminus, the populations will still be far closer genetically to those on the western pole than those just to the east!

 

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MORE ABOUT: Race

The social and biological construction of race

By Razib Khan | February 12, 2012 2:45 pm

Many of our categories are human constructions which map upon patterns in nature which we perceive rather darkly. The joints about which nature turns are as they are, our own names and representations are a different thing altogether. This does not mean that our categories have no utility, but we should be careful of confusing empirical distributions, our own models of those distributions, and reality as it is stripped of human interpretative artifice.

I have argued extensively on this weblog that:

1) Generating a phylogeny of human populations and individuals within those populations is trivial. You don’t need many markers, depending on the grain of your phylogeny (e.g., to differentiate West Africans vs. Northern Europeans you actually can use one marker!).

2) These phylogenies reflect evolutionary history, and the trait differences are not just superficial (i.e., “skin deep”).

The former proposition I believe is well established. A group such as “black American” has a clear distribution of ancestries in a population genetic sense. The latter proposition is more controversial and subject to contention. My own assumption is that we will know the truth of the matter within the generation.

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CATEGORIZED UNDER: Anthroplogy, Population Genetics
MORE ABOUT: Hispanics, Latinos, Race

1 migrant needed to prevent genetic divergence

By Razib Khan | January 26, 2012 2:09 am

In the survey below I asked if you knew about how many migrants per generation were needed to prevent divergence between populations. About ~80 percent of you stated you did not know the answer. That was not totally surprising to me. The reason I asked is that the result is moderately obscure, but also rather surprisingly simple and fruitful. The rule of thumb is that 1 migrant per generation is needed to prevent divergence.*

It doesn’t tell you much in and of itself of course. But if you think about it you can inject that fact into all sorts of other population genetic phenomena. For example, to have selection across two populations which is not reducible to selection within those populations (i.e., inter-demic selection) you need group-level genetic differences. These differences can be measured by the Fst statistic. In short the value of Fst tells you the proportion of variation which can be attributed to between-group differences (e.g., Fst across human races is ~0.15). For natural selection to have any adaptive effect you also need heritable variation. If you have lots of heritable variation selection can be weaker, while if you have little heritable variation selection has to be very strong (see response to selection). Fst is a rough gauge of heritable variation when you are evaluating group level differences. An Fst of 1.0 would imply that the groups are nearly perfectly distinct at the loci of interest, while an Fst of 0.0 would imply that the groups are not genetically distinct at all. With no distinction selection would have no efficacy in terms of driving adaptation. All this is a long way to saying that the 1 migrant rule is one reason that evolutionary biologists take a skeptical position in relation to group selection. It tends to quickly erase the variation which group selection depends upon.

 

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CATEGORIZED UNDER: Population Genetics

Nature really is real

By Razib Khan | December 18, 2011 2:30 am

I generated the figure at left from table 9.6 in The Genetics of Human Populations. This book was published in 1971, but I purchased the 1999 edition (which was simply a republication of the original text by Dover) in 2005.* At the time I recall reading the section on inferring the number of genetic loci implicated in the variation in pigmentation with some mild skepticism. The authors, L. L. Cavalli-Sforza and W. F. Bodmer pegged the black-white difference due to ~4 genes. Their data set consisted of individuals of various races in Liverpool; whites, blacks, people with one white parent and one black parent (F1 hybrids), people with three grandparents of one race and one of another (“backcrosses,” where you take an F1 and mate them with one of the parental lines), and finally, F2 individuals who are the product of pairings of F1s.

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MORE ABOUT: Human Genetics

James F. Crow in Genetics

By Razib Khan | December 16, 2011 12:03 am

At 95 James F. Crow is not only an eminent population geneticist, but he knew the figures who were responsible for the whole field. The journal Genetics has commissioned a series of essays and perspectives in his honor. The first is by Daniel Hartl. I thought this was funny:

Soon after joining the program I asked Professor Crow whether I could join his lab as a graduate student. He thought for a moment and then said, “Yes, Dan, provided you understand that population genetics is a recondite field that will never be of great interest except to a small group of specialists.” I remember this because afterward I hurried to look up “recondite” in the dictionary. His admonition made population genetics seem like some variety of monasticism, which, being an admirer of Gregor Mendel, was all right by me. Little did either of us foresee that genetics would be transformed in our lifetimes by genomic sequencing on a population scale and the development of computer technologies capable of analyzing terabytes of data and that population genetics would become a key approach for understanding human evolutionary history as well as for identifying genetic risk factors for common diseases.

I had the privilege of interviewing Crow in 2006. My email requesting an interview was sent only on the smallest probability of a reply, but he replied immediately! And when I sent my questions again the reply was nearly immediate. My favorite of Crow’s answers: “In my view it is wrong to say that research in this area — assuming it is well done — is out of order. I feel strongly that we should not discourage a line of research because someone might not like a possible outcome.” At his age he’s seen many fashions come and go. But nature abides and persists.

CATEGORIZED UNDER: Population Genetics
MORE ABOUT: James F. Crow

On the real possibility of human differences

By Razib Khan | November 26, 2011 1:16 pm

I have discussed the reality that many areas of psychology are susceptible enough to false positives that the ideological preferences of the researchers come to the fore. CBC Radio contacted me after that post, and I asked them to consider that in 1960 psychologists discussed the behavior of homosexuality as if it was a pathology. Is homosexuality no longer a pathology, or have we as a society changed our definitions? In any given discipline when confronted with the specter of false positives which happen to meet statistical significance there is the natural tendency to align the outcome so that it is socially and professionally optimized. That is, the results support your own ideological preferences, and, they reinforce your own career aspirations. Publishing preferred positive results furthers both these ends, even if at the end of the day many researchers may understand on a deep level the likelihood that a specific set of published results are not robust.

This issue is not endemic to social sciences alone. I have already admitted this issue in medical sciences, where there is a lot of money at stake. But it crops up in more theoretical biology as well. In the early 20th century Charles Davenport’s research which suggested the inferiority of hybrids between human races was in keeping with the ideological preferences of the era. In our age Armand Leroi extols the beauty of hybrids, who have masked their genetic load through heterozygosity (a nations like Britain which once had a public norm against ‘mongrelization’ now promote racial intermarriage in the dominant media!). There are a priori biological rationales for both positions, hybrid breakdown and vigor (for humans from what I have heard and seen there seems to be very little evidence overall for either once you control for the deleterious consequences of inbreeding). In 1900 and in 2000 there are very different and opposing social preferences on this issue (as opposed to individual preferences). The empirical distribution of outcomes will vary in any given set of cases, so researchers are incentivized to seek the results which align well with social expectations. (here’s an example of heightened fatality due to mixing genetic backgrounds; it seems the exception rather than the rule).

Thinking about all this made me reread James F. Crow’s Unequal by nature: a geneticist’s perspective on human differences. Crow is arguably the most eminent living population geneticist (see my interview from 2006). Born in 1916, he has seen much come and go. For those of us who wonder how anyone could accept ideas which seem shocking or unbelievable today, I suspect Crow could give an answer. He was there. In any case, on an editorial note I think the essay should have been titled “Different by nature.” Inequality tends to connote a rank order of superiority or inferiority, though in the context of the essay the title is obviously accurate. Here is the most important section:

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When did population genetics emerge?

By Razib Khan | October 6, 2011 12:49 pm

I recently heard an eminent geneticist declare that population genetics began with Theodosius Dobzhansky’s Genetics and the Origin of Species in 1937. My immediate reflex was to be skeptical of this, at least going by Will Provine’s treatment in The Origins of Theoretical Population Genetics, which seemed to push back the timing to the 1920s.

So I looked up “population genetics” in Ngram viewer.

 

 
These results are not consistent with my expectations. Looks like my intuition was wrong. At least for the term population genetics. Score one for experience and wisdom.

CATEGORIZED UNDER: Population Genetics
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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