Razib Khan One-stop-shopping for all of my content

March 19, 2017

10 things about human evolution (genetics) you should know (simpler)

Filed under: Evolution — razibk @ 3:25 am

In response to my earlier post some people suggested that the language was impenetrable. Nathan Taylor​ offered to make it more plain spoken, so here is this go at it. I think it’s pretty good.

(text below is from Nathan)  

1) Modern humans stayed in Africa for tens of thousands years of before expanding beyond it. Most of the ancestors of non-African humanity seem to have started expanding rapidly from a small founder group of less than 1,000 people, starting around 50-75 thousand years years ago. African humanity has a more complex pattern. Some groups diverged as early as 200,000 years ago, then mixed back together.


2) Don’t think of humanity as a branching tree. Rather think of humanity as groups of streams. Some streams end, many fold back on one another, and some suddenly have massive expansions. Surprisingly, all major human population groups we know today seem to be the product of relatively recent fusions. Even Africa, the source of modern humanity, has seen streams flow back from Eurasia.


3) Many of the characteristics people focus on today are of recent origin. At least as measured in thousands or tens of thousands of years. 8,000 years ago parts of Europe were populated by brown skinned hunter gatherers with blue eyes. Whiter skin is a (relatively) recent development. And the thick straight hair now common among East Asians is recent as well.

4) The genetic variant which helps Tibetans tolerate very high altitudes comes from a human lineage as divergent from modern humans as Neanderthals are. The Denisovans. This illustrates a general trend: we have adaptations from other very diverged human lineages in our genes today. Even if the genetic percentage is small.


5) The transition to agriculture and complex civilization seems correlated with the explosive growth of a few select male Y chromosomes. Think Genghis Khan.


6) It seems unlikely there is one genetic change which made humans humans. This is less certain than 1-5, but I’m pretty sure it’s true. Researchers have been looking for this for years and haven’t turned up anything definitive. I think the reason is simple enough: many genetic changes came together to make us distinctive.


7) A lot of variation between human groups is not due to novel genes. Rather it comes from increasing the popularity of pre-existing genetic variants. For example, the lightening of skin across parts of Eurasia is due to an increase of genetic variants which are common to many human populations. Height is another example.


8) Cultural flexibility does not means humans are not evolving. On the contrary, strong shifts in cultural norms seem to drive human evolution. Lactase persistence (the ability to drink milk as an adult) is a clear case. But even genetic tolerance to malaria was ultimately driven by human created environmental changes.


9) There are no “most ancient” human group. By definition, we are all equally separated in time from our common ancestors.


10) There are hints of possible new discoveries coming from ancient human DNA.  For example there is evidence of humans leaving Africa ~100,000 years ago into Eurasia in both genetic and fossil data. These earlier humans may have been overrun by a later group. But this is hard to determine with the current data. The DNA of current and ancient humans still has many stories to tell.

10 things about human evolution (genetics) you should know

Filed under: Evolution — razibk @ 1:53 am

In 2011 I had dinner with a friend of mine from college. He’s a smart guy. Ph.D. in chemistry form M.I.T and all that. I mentioned offhand how it was rather proven to good degree of certainty there was Neanderthal gene flow into modern humans (our lineage)[1]​. He was somewhat surprised by this information, and I was aghast that he didn’t know. 1It was one of the biggest science stories of the year. Right?

What that brought home to me is that something that seems revolutionary near to your heart or field of occupational interest may not be so visible to those who are not similarly situated. My friend is a well educated person with a science Ph.D., but it was just not on his radar. Similarly, I had very smart friends in college who were evangelical Christians who were surprised by the high degree of identity between the chimpanzee and human in regards to our DNA sequence (they were Creationists, and skeptical of any close kinship).

Here’s a final example that might interest readers. I had a long conversation with a relatively prominent journalist a month or so ago. Someone who writes in biology, and in particular genetics (who is not Carl Zimmer). I mentioned offhand to them that the work of various labs utilizing ancient DNA is showing rather conclusively that the vast majority of human populations are relatively recent admixtures between highly diverged lineages. To put it in plainer language: we are all mestizos! This journalist was totally surprised by this fact.

This indicates to me again that facts which are “known” in the “in-group” may be surprising to those who are not as hooked in. It isn’t a matter of being educated, smart, or interested. It’s a matter of narrowly constrained social channels.

Here are 10 facts that we’ve recently discovered about human evolution, with a focus on genetics since that’s what I know best, which you should probably know. Or might find interesting.

1) The expansion/development of modern humans occurred within Africa for tens of thousands of before their expansion “Out of Africa.” Most of the ancestors of non-African humanity seem to have started expanding rapidly from a small founder group of 100-1,000 50-75 thousand years years ago. African humanity has a different and more complex historical pattern, with lineages which began diverging as early as 200,000 years before the present, and then mixing back with each other.

2) Related to #1, we’re one species, so rather than an expanding “tree” from common ancestors, it’s better to think of a mesh which keeps coming back together, as some branches are pruned, and the whole pulses out periodically. All major human populations seem to be the product of relatively recent fusions between diverged branches. Africa was the source of modern humanity, but clearly there has been “back migration” from Eurasia.

3) Many of the phenotypes we define as characteristic of various human populations are relatively recent. E.g., the depigmented look of Northern Europeans, or the thick straight hair of East Asians.

4) The Denisovan version of EPAS1 which is found in Tibetans illustrates a general trend: we have adaptations from other very diverged human lineages through low levels of gene flow[2]​.

5) The transition to agriculture and complex “civilization” seems correlated to pulses of highly fecund male paternal lineages. Many of the common Y chromosomes today exhibit a pattern of diversification indicative of explosive population growth.

6) It seems unlike there is one singular genetic change which makes us sui generis or distinctive in relation to our hominin cousins. This is less certain than 1-5, but I’m pretty sure that this is so. Researchers have been looking for years, and not finding anything definitive, and I think there’s a reason. There isn’t anything definitive. Many genetic changes come together to make our lineage distinctive.

7) A lot of adaptation occurs through reemergence of old variation which is floating around in the human population. For example, the lightening of skin across parts of Eurasia co-opt common mammalian pigmentation pathways.

8) Cultural flexibility does not negate biological evolution. On the contrary, strong shifts in cultural norms seem to drive biology. Lactase persistence is a clear case, but even something like malaria adaptation is ultimately due to anthropogenic environmental changes.

9) We are all equally descended from common ancestors. There are no “most ancient” human lineages. We’re all equally recent by definition.

10) There are evolutionary genetic events in our history which are hinted at in the most recent data, so there are major lacunae in our knowledge. The picture is well formed, but not complete. E.g., there is evidence of pulses out of Africa ~100,000 years ago into Eurasia in both genetic and fossil data. These lineages may have gone extinct, or, their contribution may be difficult to detect with current data sets. But there is clearly more to be told in this story.

November 13, 2013

The color of life as a coincidence

Filed under: Anthroplogy,Evolution,Evolutionary Genetics,Genetics of taste,Taste — Razib Khan @ 12:35 am

Credit: Eric Hunt

Credit: Eric Hunt

I do love me some sprouts! Greens, bitters, strong flavors of all sorts. I’ve always been like this. Some of this is surely environment. My family comes from a part of South Asia known for its love of bracing and bold sensation. But perhaps I was born this way? There’s a fair amount of evidence that taste has a substantial genetic component. This does not mean genes determine what one tastes, but it certainly opens the door for passive gene-environment correlations. If you do not find a flavor offensive, you are much more likely to explore it depths, and cultivate your palette.

220px-Durio_kutej_F_070203_ime

Dost thou dare?
Credit: W.A. Djatmiko

And of course I’m not the only one with a deep interest in such questions. With the marginal income available to us many Americans have become “foodies,” searching for flavor bursts and novelties which their ancestors might never have been able to comprehend. More deeply in a philosophical sense the question of qualia reemerges if there is a predictable degree of inter-subjectivity in taste perception (OK, qualia is always there, though scientific sorts tend to view it as intractable in a fundamental sense).


But there’s heritability, and then there’s genes. We know that perception in some ways is heritable, but what is perhaps more interesting is if you can peg a specific genomic location to it. Then the evolutionary story becomes all the richer. And so it is with the locus TAS2R16, where a nonsynonymous mutation at location 516 seems to result in heightened sensitivity to bitter tastes. More specifically, it’s rs846664, and the derived T allele is fixed outside of Africa, while the ancestral G allele still segregates at appreciable fractions within African populations. A new paper in Molecular Biology and Evolution puts this locus under a microscope, though it does not come up with any clear conclusions. Origin and Differential Selection of Allelic Variation at TAS2R16 Associated with Salicin Bitter Taste Sensitivity in Africa presents some interesting findings. First, let’s look at the distribution of the variation in their sample populations at the SNP of most particular interest:

Region Population T516G
Outside of Africa Non-Africans 0.000
Ethiopia Semitic 0.059
Tanzania Sandawe 0.083
Ethiopia Omotic 0.093
Ethiopia Cushitic 0.095
Tanzania Iraqw 0.111
West Central Africa Fulani 0.114
Kenya Niger-Kordofanian 0.133
Ethiopia Nilo-Saharan 0.156
Kenya Afroasiatic 0.162
West Central Africa Niger-Kordofanian 0.214
Kenya Nilo-Saharan 0.225
Kenya Luo 0.250
Central Africa Niger-Kordofanian 0.329
Tanzania Hadza 0.333
Central Africa Bulala 0.361
Central Africa Nilo-Saharan 0.367
West Central Africa Afroasiatic 0.462
West Central Africa Nilo-Saharan 0.500

As you can see T is fixed outside of Africa, and varies across many African populations  Previous work implied this, though coverage within Africa was not good. One thing to observe though is that the frequency of A within Africa can not be explained by recent Eurasian admixture. The frequency is way too high for that to be the sole explanation, and in any case there is no evidence that ~33% of the Hadza’s ancestry is of Eurasian provenance (the Hadza being one of the three major groups of African hunter-gatherers, along with the Bushmen and Pygmies).

Within the paper the authors resequenced ~1,000 base pairs across diverse African populations in an exonic region of this gene (the stuff that codes for amino acids). What they discovered is that of the SNPs segregating, 516 in particular was critical toward effecting phenotyping change. Not only did individuals with the T variant notably exhibit stronger bitter sensitivity, but in vitro expression with a reporter was elevated. Because they had such a dense genomic region they could perform various nucleotide based tests to detect natural selection, and, attempt coalescent models to infer genealogical history.

I’m going to spare you some of the gory details at this point. Here’s what they found. First, it does look like the region is under natural selection in many African populations, in particular, the derived haplotype with T at 516 at the center. But this result is not reproduced across all tests. The coalescent simulations make clear why: the mutation is an old variant with deep roots in the hominin lineage. In other words this variation pre-dates H. sapiens. It looks like the T allele has rapidly increased in frequency relatively recently, though more on the order of ~50,000 years, rather than ~10,000.* Basically around the time of the “Out of Africa” event. Additionally, there’s a tell-tale sign that this is being subject to selection within Africa: the genetic differences across populations at TAS2R16 far exceed the genome-wide values (the Fst at this locus is in the top 1% of loci within the African genome). Finally, one should note that the G allele haplotypes seem to be much more strongly constrained, as if they’re under purifying selection. This means that the switch to T is not all gain.

At this point you may be ready for a story about how some African populations, like Eurasians, underwent a lifestyle change, and diet changes resulted in a shift in sensory perception. That does not seem to be the story. Rather, the authors did not seem to be able to agree upon a neat explanation for what is driving these recent sweeps up from ancient standing genetic variation. They do observe that the variation does tend to cluster geographically, more so than the genome-wide results would imply. There’s likely some adaptation going on, they simply don’t know what. In the introduction and elsewhere you can see that variation at TAS2R16 does correlate with other traits. Not too surprising due to the relatively ubiquity of pleiotropy; one gene with many effects.

Stepping outside of the implications of this specific result, let’s think about what might be a takeaway: something as essential as taste perception might be a side effect of other aspects of evolutionary processes. In other words, we don’t know what the phenotypic target of selection is in this case, but we do have a good handle one of the major side effects, which is sensory perception. How one taste seems like a big deal.** Andthere have been many theories propounded that variation in bitter sensitivity is due to adaptation to poisonous plants and such, but really no one knew, and that was just the most plausible of low hanging fruit. With these results from Africa, where there is more variation in the trait and genes, and good geographic coverage, that seems to be an implausible model to adhere to (one would think the hunter-gatherer Hadza would exhibit the most sensitivity, no?). Many of the traits and tendencies which we humans see as fundamental, essential, and of great import, many actually be side effects of powerful evolutionary forces hammering at the genetic-correlation matrices which define the hidden network of co-dependencies within the genome. So there, I said it. Life is an accident. Enjoy it.

Citation: Campbell, Michael C., et al. “Origin and Differential Selection of Allelic Variation at TAS2R16 Associated with Salicin Bitter Taste Sensitivity in Africa.” Molecular biology and evolution (2013): mst211.

* If it was closer to ~10,000 I think haplotype based tests would come back with something, but they do not.

** Some Epicureans might be accused of reducing the good to taste!

The post The color of life as a coincidence appeared first on Gene Expression.

The color of life as a coincidence

Filed under: Anthroplogy,Evolution,Evolutionary Genetics,Genetics of taste,Taste — Razib Khan @ 12:35 am

Credit: Eric Hunt

Credit: Eric Hunt

I do love me some sprouts! Greens, bitters, strong flavors of all sorts. I’ve always been like this. Some of this is surely environment. My family comes from a part of South Asia known for its love of bracing and bold sensation. But perhaps I was born this way? There’s a fair amount of evidence that taste has a substantial genetic component. This does not mean genes determine what one tastes, but it certainly opens the door for passive gene-environment correlations. If you do not find a flavor offensive, you are much more likely to explore it depths, and cultivate your palette.

220px-Durio_kutej_F_070203_ime

Dost thou dare?
Credit: W.A. Djatmiko

And of course I’m not the only one with a deep interest in such questions. With the marginal income available to us many Americans have become “foodies,” searching for flavor bursts and novelties which their ancestors might never have been able to comprehend. More deeply in a philosophical sense the question of qualia reemerges if there is a predictable degree of inter-subjectivity in taste perception (OK, qualia is always there, though scientific sorts tend to view it as intractable in a fundamental sense).


But there’s heritability, and then there’s genes. We know that perception in some ways is heritable, but what is perhaps more interesting is if you can peg a specific genomic location to it. Then the evolutionary story becomes all the richer. And so it is with the locus TAS2R16, where a nonsynonymous mutation at location 516 seems to result in heightened sensitivity to bitter tastes. More specifically, it’s rs846664, and the derived T allele is fixed outside of Africa, while the ancestral G allele still segregates at appreciable fractions within African populations. A new paper in Molecular Biology and Evolution puts this locus under a microscope, though it does not come up with any clear conclusions. Origin and Differential Selection of Allelic Variation at TAS2R16 Associated with Salicin Bitter Taste Sensitivity in Africa presents some interesting findings. First, let’s look at the distribution of the variation in their sample populations at the SNP of most particular interest:

Region Population T516G
Outside of Africa Non-Africans 0.000
Ethiopia Semitic 0.059
Tanzania Sandawe 0.083
Ethiopia Omotic 0.093
Ethiopia Cushitic 0.095
Tanzania Iraqw 0.111
West Central Africa Fulani 0.114
Kenya Niger-Kordofanian 0.133
Ethiopia Nilo-Saharan 0.156
Kenya Afroasiatic 0.162
West Central Africa Niger-Kordofanian 0.214
Kenya Nilo-Saharan 0.225
Kenya Luo 0.250
Central Africa Niger-Kordofanian 0.329
Tanzania Hadza 0.333
Central Africa Bulala 0.361
Central Africa Nilo-Saharan 0.367
West Central Africa Afroasiatic 0.462
West Central Africa Nilo-Saharan 0.500

As you can see T is fixed outside of Africa, and varies across many African populations  Previous work implied this, though coverage within Africa was not good. One thing to observe though is that the frequency of A within Africa can not be explained by recent Eurasian admixture. The frequency is way too high for that to be the sole explanation, and in any case there is no evidence that ~33% of the Hadza’s ancestry is of Eurasian provenance (the Hadza being one of the three major groups of African hunter-gatherers, along with the Bushmen and Pygmies).

Within the paper the authors resequenced ~1,000 base pairs across diverse African populations in an exonic region of this gene (the stuff that codes for amino acids). What they discovered is that of the SNPs segregating, 516 in particular was critical toward effecting phenotyping change. Not only did individuals with the T variant notably exhibit stronger bitter sensitivity, but in vitro expression with a reporter was elevated. Because they had such a dense genomic region they could perform various nucleotide based tests to detect natural selection, and, attempt coalescent models to infer genealogical history.

I’m going to spare you some of the gory details at this point. Here’s what they found. First, it does look like the region is under natural selection in many African populations, in particular, the derived haplotype with T at 516 at the center. But this result is not reproduced across all tests. The coalescent simulations make clear why: the mutation is an old variant with deep roots in the hominin lineage. In other words this variation pre-dates H. sapiens. It looks like the T allele has rapidly increased in frequency relatively recently, though more on the order of ~50,000 years, rather than ~10,000.* Basically around the time of the “Out of Africa” event. Additionally, there’s a tell-tale sign that this is being subject to selection within Africa: the genetic differences across populations at TAS2R16 far exceed the genome-wide values (the Fst at this locus is in the top 1% of loci within the African genome). Finally, one should note that the G allele haplotypes seem to be much more strongly constrained, as if they’re under purifying selection. This means that the switch to T is not all gain.

At this point you may be ready for a story about how some African populations, like Eurasians, underwent a lifestyle change, and diet changes resulted in a shift in sensory perception. That does not seem to be the story. Rather, the authors did not seem to be able to agree upon a neat explanation for what is driving these recent sweeps up from ancient standing genetic variation. They do observe that the variation does tend to cluster geographically, more so than the genome-wide results would imply. There’s likely some adaptation going on, they simply don’t know what. In the introduction and elsewhere you can see that variation at TAS2R16 does correlate with other traits. Not too surprising due to the relatively ubiquity of pleiotropy; one gene with many effects.

Stepping outside of the implications of this specific result, let’s think about what might be a takeaway: something as essential as taste perception might be a side effect of other aspects of evolutionary processes. In other words, we don’t know what the phenotypic target of selection is in this case, but we do have a good handle one of the major side effects, which is sensory perception. How one taste seems like a big deal.** Andthere have been many theories propounded that variation in bitter sensitivity is due to adaptation to poisonous plants and such, but really no one knew, and that was just the most plausible of low hanging fruit. With these results from Africa, where there is more variation in the trait and genes, and good geographic coverage, that seems to be an implausible model to adhere to (one would think the hunter-gatherer Hadza would exhibit the most sensitivity, no?). Many of the traits and tendencies which we humans see as fundamental, essential, and of great import, many actually be side effects of powerful evolutionary forces hammering at the genetic-correlation matrices which define the hidden network of co-dependencies within the genome. So there, I said it. Life is an accident. Enjoy it.

Citation: Campbell, Michael C., et al. “Origin and Differential Selection of Allelic Variation at TAS2R16 Associated with Salicin Bitter Taste Sensitivity in Africa.” Molecular biology and evolution (2013): mst211.

* If it was closer to ~10,000 I think haplotype based tests would come back with something, but they do not.

** Some Epicureans might be accused of reducing the good to taste!

The post The color of life as a coincidence appeared first on Gene Expression.

October 27, 2013

Our forefathers were fierce & our foremothers were faithful

Filed under: Cuckoldry,Evolution — Razib Khan @ 5:51 pm

Credit: Chineeb

Credit: Chineeb

One of the peculiarities of human historical genetics is that people can simultaneously accept the existence of aggressive polygynous males such as Genghis Khan, and promiscuous females who give rise to the idea that 1 out of 10 children have an incorrect assigned paternity. I’ve mentioned the cuckoldry myth before. It is a common evolutionary myth; I’ve heard many biologists quote the 1 out of 10 number, and have often made myself obnoxious by pointing to the contradictory literature in this area. This isn’t to say that cuckoldry doesn’t exist. There’s certainly an evolutionary reason so many males engage in “mate guarding.” But you don’t need a high frequency of a trait to allow it to be selectively constrained. If it’s deleterious, then it will be driven down in frequency rather quickly. Whenever you get outbreaks of males who are sanguine about providing resources for offspring who are not their biological issue, natural selection will kick in and guarantee that this generous spirit toward their cheating partners and the delinquent cads does not persist.


The way that modern genetics adds value to this area is that one can compare Y chromosomal lineages to surnames. The logic is simple. If you have a constant frequency of misattributed paternity per generation over time the correlation between a surname and a Y chromosomal lineage will weaken. In addition, because the interlopers are likely to be different from each other you’ll have a pattern with (for example) ~50% of the male individuals of a given surname may carry one haplotype, while the other ~50% are distributed across hundreds of other haplotypes (one can imagine twists on the scenario, for example an early interloper might result in a secondary highly frequent haplotype).

So here’s an new study to bury this tired old urban myth, Low historical rates of cuckoldry in a Western European human population traced by Y-chromosome and genealogical data:

Overall, our results provide the first large-scale, unbiased genetic study of historical EPP rates in a human Western European population, with two independent estimation methods giving largely concordant results. Using the most direct estimation method, based on pairs of males that had a GCA in the last few centuries, we estimated the average EPP rate at 0.91% per generation (95% CI: lower bound 0.41% and upper bound 1.75%). This method took advantage of the hypervariability and mutability of Y-STR haplotypes, and the high phylogenetic resolution of the used Y-SNP haplogroups, which allowed paternally unrelated males to be easily recognized as such [35]. In addition, using a second method that was based on the population genetic traces of a past immigration event which happened at the end of the sixteenth century, we estimated the EPP rate at around 2%. Although this estimate had a broader CI (upper 95% confidence limit = 8%), the actual estimate was close to the first one.

Both of our methods therefore estimated a substantially lower historical EPP rate for Flanders than the 8–30% per generation suggested by previous studies based on behavioural data on rates of EPCs in Western Europe and given the absence of reliable contraceptive methods [30–33]….

It’s open access, so read the whole thing if you aren’t convinced.

The authors are clear that this is from a sample in Flanders, but I do not find that this population should be that exceptional across the Eurasian Ecumene. In other words, I’ll be willing to put down money that Indian gotras and Chinese patrlineal clans will exhibit the same pattern of cuckoldry frequency. Additionally, the authors note that this pattern of high paternity confidence is paired with male investment in offspring. That seems relatively typical among many members of our species, though the extent seems to vary by population and environmental condition.

The post Our forefathers were fierce & our foremothers were faithful appeared first on Gene Expression.

Our forefathers were fierce & our foremothers were faithful

Filed under: Cuckoldry,Evolution — Razib Khan @ 5:51 pm

Credit: Chineeb

Credit: Chineeb

One of the peculiarities of human historical genetics is that people can simultaneously accept the existence of aggressive polygynous males such as Genghis Khan, and promiscuous females who give rise to the idea that 1 out of 10 children have an incorrect assigned paternity. I’ve mentioned the cuckoldry myth before. It is a common evolutionary myth; I’ve heard many biologists quote the 1 out of 10 number, and have often made myself obnoxious by pointing to the contradictory literature in this area. This isn’t to say that cuckoldry doesn’t exist. There’s certainly an evolutionary reason so many males engage in “mate guarding.” But you don’t need a high frequency of a trait to allow it to be selectively constrained. If it’s deleterious, then it will be driven down in frequency rather quickly. Whenever you get outbreaks of males who are sanguine about providing resources for offspring who are not their biological issue, natural selection will kick in and guarantee that this generous spirit toward their cheating partners and the delinquent cads does not persist.


The way that modern genetics adds value to this area is that one can compare Y chromosomal lineages to surnames. The logic is simple. If you have a constant frequency of misattributed paternity per generation over time the correlation between a surname and a Y chromosomal lineage will weaken. In addition, because the interlopers are likely to be different from each other you’ll have a pattern with (for example) ~50% of the male individuals of a given surname may carry one haplotype, while the other ~50% are distributed across hundreds of other haplotypes (one can imagine twists on the scenario, for example an early interloper might result in a secondary highly frequent haplotype).

So here’s an new study to bury this tired old urban myth, Low historical rates of cuckoldry in a Western European human population traced by Y-chromosome and genealogical data:

Overall, our results provide the first large-scale, unbiased genetic study of historical EPP rates in a human Western European population, with two independent estimation methods giving largely concordant results. Using the most direct estimation method, based on pairs of males that had a GCA in the last few centuries, we estimated the average EPP rate at 0.91% per generation (95% CI: lower bound 0.41% and upper bound 1.75%). This method took advantage of the hypervariability and mutability of Y-STR haplotypes, and the high phylogenetic resolution of the used Y-SNP haplogroups, which allowed paternally unrelated males to be easily recognized as such [35]. In addition, using a second method that was based on the population genetic traces of a past immigration event which happened at the end of the sixteenth century, we estimated the EPP rate at around 2%. Although this estimate had a broader CI (upper 95% confidence limit = 8%), the actual estimate was close to the first one.

Both of our methods therefore estimated a substantially lower historical EPP rate for Flanders than the 8–30% per generation suggested by previous studies based on behavioural data on rates of EPCs in Western Europe and given the absence of reliable contraceptive methods [30–33]….

It’s open access, so read the whole thing if you aren’t convinced.

The authors are clear that this is from a sample in Flanders, but I do not find that this population should be that exceptional across the Eurasian Ecumene. In other words, I’ll be willing to put down money that Indian gotras and Chinese patrlineal clans will exhibit the same pattern of cuckoldry frequency. Additionally, the authors note that this pattern of high paternity confidence is paired with male investment in offspring. That seems relatively typical among many members of our species, though the extent seems to vary by population and environmental condition.

The post Our forefathers were fierce & our foremothers were faithful appeared first on Gene Expression.

November 11, 2012

Reflections on the evolution at ASHG 2012

As most readers know I was at ASHG 2012. I’m going to divide this post in half. First, the generalities of the meeting. And second, specific posters, etc.

Generalities:

- Life Technologies/Ion Torrent apparently hires d-bag bros to represent them at conferences. The poster people were fine, but the guys manning the Ion Torrent Bus were total jackasses if they thought it would be funny/amusing/etc. Human resources acumen is not always a reflection of technological chops, but I sure don’t expect organizational competence if they (HR) thought it was smart to hire guys who thought (the d-bags) it would be amusing to alienate a selection of conference goers at ASHG. Go Affy & Illumina!

- Speaking of sequencing, there were some young companies trying to pitch technologies which will solve the problem of lack of long reads. I’m hopeful, but after the Pacific Biosciences fiasco of the late 2000s, I don’t think there’s a point in putting hopes on any given firm.

- I walked the poster hall, read the titles, and at least skimmed all 3,000+ posters’ abstracts. No surprise that genomics was all over the place. But perhaps a moderate ...

September 17, 2012

The feathery Neandertal

Filed under: Evolution,Neandertal — Razib Khan @ 10:11 pm

Birds of a Feather: Neanderthal Exploitation of Raptors and Corvids:

The hypothesis that Neanderthals exploited birds for the use of their feathers or claws as personal ornaments in symbolic behaviour is revolutionary as it assigns unprecedented cognitive abilities to these hominins. This inference, however, is based on modest faunal samples and thus may not represent a regular or systematic behaviour. Here we address this issue by looking for evidence of such behaviour across a large temporal and geographical framework. Our analyses try to answer four main questions: 1) does a Neanderthal to raptor-corvid connection exist at a large scale, thus avoiding associations that might be regarded as local in space or time?; 2) did Middle (associated with Neanderthals) and Upper Palaeolithic (associated with modern humans) sites contain a greater range of these species than Late Pleistocene paleontological sites?; 3) is there a taphonomic association between Neanderthals and corvids-raptors at Middle Palaeolithic sites on Gibraltar, specifically Gorham’s, Vanguard and Ibex Caves? and; 4) was the extraction of wing feathers a local phenomenon exclusive to the Neanderthals at these sites or was it a geographically wider phenomenon?. We compiled a database of 1699 Pleistocene Palearctic sites based on fossil bird sites. We ...

September 16, 2012

What the substrate tells

Filed under: Evolution,Evolutionary Genetics,Genetics,Genomics — Razib Khan @ 7:26 pm

One of the weird things about genetics is that it encompasses both the abstract and the concrete. The formal and physical. You can talk to a geneticist who is mostly interested in details of molecular mechanisms, and is steeped in structural biology. For these people genes are specific and material things. In contrast there are other geneticists who focus more on genes as units of analysis. In this case genes are semantic labels for the mediators within an intersection of phenomena. Recall that genetics predates the knowledge of its concrete substrate by 50 years! By the 1920s Mendelian genetics had been fused with evolutionary biology to create a systematic framework in which we could understand the patterns of inheritance across the generations. In the 1950s the DNA revolution was upon us, but as W. D. Hamilton recalls this had only a minimal impact on the evolutionary genetic thinkers of the era. With the Lewontin and Hubby allozyme paper in the mid-1960s this sort of benign disciplinary evasion was no longer possible; the field of molecular evolution came into its own.*

Today with genomics these human-imposed artificialities are fading away. Consider the concept of genetic recombination. Originally an ...

September 12, 2012

An ontology of genetic diversity

Filed under: Evolution,Evolutionary Genetics — Razib Khan @ 11:23 pm

Implicit in the title The Origin Of Species is the question: why the plural? In other words, why isn’t there a singular apex species which dominates this planet? One can imagine an abstract system where natural selection slowly but gradually sifts through variation and designs a best-of-all-replicators. And yet on the contrary it seems that our planet has exhibited an overall tendency of going from lower to higher diversity. The age of stromatolites may be the last epoch when we had the best-of-all-replicators.


These sorts of deep questions about variation drive many of the research projects in evolutionary biology. Often one focuses on a narrow zone of interest. An organism for example which might serve as an illustrative model for more general processes. Or, a particular dynamic which interlocks with other processes to form a whole phenomenon. But on occasion you have to sit and ponder the whole shebang. Why genetic diversity? More specifically, why not more diversity of genetic diversity? The issue here is what is sometimes termed Lewontin’s paradox.

Consider two populations. One population goes through an extreme bottleneck, while the other maintains a large population over the generations. What would you presume in regards to ...

August 29, 2012

Evolution: its ideological own refutation

Filed under: Evolution — Razib Khan @ 10:24 pm

 

Recently I stumbled upon the fact that Honey Boo Boo‘s sister had a child at age 18. The grandmother, Honey Boo Boo’s mother, is 33 years old. Younger than I am! Then I see headlines in trashy British tabloids of the form: The three men who have fathered 78 children with 46 different women… and they’re not paying child support to any of them. Here I am, in the fullness of man-childhood, a new father, groping to understand evolutionary process in all its glory, and here are they who live evolution! There are those around us who don’t blink at maximizing their fitness in the modern world. Here’s some data from the GSS:

Humans developed from animals Number of children 0 1 2 3 4 5 6 or more TRUE 64.2 55.6 50.7 41.5 35.1 40.7 32.2 FALSE 35.8 44.4 49.3 58.5 64.9 59.3 67.8

Age when first child born
18 and under 19 to 24 25 to 29 30 to 34 35 and above

TRUE 56.6 40.1 54.2 59.2 68
FALSE 43.4 59.9 45.8 40.8 32

Go teen parents! Maybe?

Evolution: its ideological own refutation

Filed under: Evolution,Idiocracy — Razib Khan @ 10:24 pm

 

Recently I stumbled upon the fact that Honey Boo Boo‘s sister had a child at age 18. The grandmother, Honey Boo Boo’s mother, is 33 years old. Younger than I am! Then I see headlines in trashy British tabloids of the form: The three men who have fathered 78 children with 46 different women… and they’re not paying child support to any of them. Here I am, in the fullness of man-childhood, a new father, groping to understand evolutionary process in all its glory, and here are they who live evolution! There are those around us who don’t blink at maximizing their fitness in the modern world. Here’s some data from the GSS:

Humans developed from animals Number of children 0 1 2 3 4 5 6 or more TRUE 64.2 55.6 50.7 41.5 35.1 40.7 32.2 FALSE 35.8 44.4 49.3 58.5 64.9 59.3 67.8

Age when first child born
18 and under 19 to 24 25 to 29 30 to 34 35 and above

TRUE 56.6 40.1 54.2 59.2 68
FALSE 43.4 59.9 45.8 40.8 32

Go teen parents! Maybe?

August 9, 2012

Why aren’t we all tall?

Filed under: Evolution,Height — Razib Khan @ 3:05 am

There’s a fair amount of social science and anecdata that tall males are more reproductively fit. More precisely, males one to two standard deviations above the norm in height seem to be at the “sweet spot” as an idealized partner (e.g., leading males). And, short men often have fewer children. Short women will pair up with tall men. Tall women will generally not pair up with shorter men. The question then has to be asked: why isn’t natural selection producing a situation where we’re all tall?

As it is, height is a highly heritable trait where there’s a lot of genetic variation present in the population. One hypothesis might be that short(er) people are simply individuals with a higher mutational load. In other words, there’s going to be variation in the load of deleterious alleles from person to person, and one’s value on quantitative traits (intelligence, height) is a reflection of one’s genetic fitness. There are problems with this model, starting with the fact that one you need to tease apart inter-population variation. Also, within families there doesn’t seem to be a correlation between height and intelligence, which you would expect to ...

July 9, 2012

Selection of and in groups

Filed under: Evolution,Social Evolution — Razib Khan @ 8:45 pm

Eric Michael Johnson has an excellent round-up of and commentary upon recent debates about “group selection” (also, a decent primer on the basics). If there is one major issue I might take with the narrative outlined, it is the idea that E. O. Wilson has made a recent about-face in regards to group selection, going from a skeptic to a believer. In Defenders of the Truth: The Sociobiology Debate Ullica Segerstrale pointed out that this was obviously not the case even in Wilson’s grand book Sociobiology. If you don’t accept this, David Sloan Wilson seems to implicitly confirm Segerstrale’s position in his semi-autobiographical book Evolution for Everyone. Finally, I’ve heard it from acquaintances at Harvard that it was an open secret that E. O. Wilson was skeptical of the “Hamiltonian orthodoxy” ascendant in evolutionary biology and ecology. The controversy over the notorious paper, The evolution of eusociality, was years in the making. From what I gather many of Wilson’s colleagues at Harvard were skeptical that he comprehended the depths of the mathematics which he promoted to support his more intuitive empirically informed skepticism of the power of inclusive fitness. It isn’t an unheard of sin ...

July 3, 2012

Why the kids don’t know no algebra

Filed under: Culture,Education,Evolution — Razib Khan @ 8:36 am

A few days ago I stumbled upon a really interesting post. And I’m wondering if my readers are at all familiar with the phenomenon outlined here (it was a total surprise to me), The myth of “they weren’t ever taught….”:

Stage One: I will describe this stage for algebra I teachers, but plug in reading, geometry, writing, science, any subject you choose, with the relevant details. This stage begins when teachers realize that easily half the class adds the numerators and denominators when adding fractions, doesn’t see the difference between 3-5 and 5-3, counts on fingers to add 8 and 6, and looks blank when asked what 7 times 3 is.

Ah, they think. The kids weren’t ever taught fractions and basic math facts! What the hell are these other teachers doing, then, taking a salary for showing the kids movies and playing Math Bingo? Insanity on the public penny. But hey, helping these kids, teaching them properly, is the reason they became teachers in the first place. So they push their schedule back, what, two weeks? Three? And go through fraction operations, reciprocals, negative numbers, the meaning of subtraction, a few properties of equality, and just wallow in the glories ...

January 25, 2012

Born to conform

Filed under: Culture,Evolution,Group Selection — Razib Khan @ 11:52 am

There is a new paper in Nature, Social networks and cooperation in hunter-gatherers, which is very interesting. As Joe Henrich observes in his view piece the panel of figure 2 (see left) is probably the most important section.

The study focuses on the Hadza, a hunter-gatherer population of Tanzania. Their language seems to be an isolate, though there have been suggestions of a connection to Khoisan. Additionally the genetic evidences tells us that like the Bushmen and Pygmies the Hadza do descend from populations which are basal to other human lineages, and were likely resident in their homeland before the arrival of farmers. And it is critical to also note that the Hadza are probably uninterrupted hunter-gatherers in terms of the history of their lifestyle, as agriculture likely arrived in Tanzania on the order of two thousand years ago, and their genetic distinctiveness indicates a separation from groups like Bantus far deeper in time. When it comes to Paleolithic model populations the Hadza are relatively “uncontaminated.”

So how does 2a matter? It shows a sharp discontinuity in cooperation across Hadza camps, all things controlled. There have been debates about the level of analysis necessary to explain human cooperation, with reductionists focused on the individual, arguing that dynamics such as kin selection and reciprocal altruism can explain the complexity we see around us simply through extension (e.g., universalist religious ideologies and philosophies usually appeal to fictive kinship or the golden rule). These data instead given some support to models which posit that group-level cultural dynamics must also be taken into account. Remember though that these more complicated systems don’t deny the importance of kin selection and reciprocal altruism; they only posit that there are other forces which can’t easily be reduced to these two.

The peculiarity of figure 2a illustrates the difference between transmission of culture, memes, and biology, genes. The Hadza are a small population, and genetically rather homogeneous in relation to their neighbors (to my knowledge they don’t exhibit much population substructure). It is difficult for between group variance to develop between human populations with adjacent residence patterns because even small amounts of migration rapidly equilibrate gene frequencies. This is why biologists have traditionally been skeptical of selection across groups. If the two entities are nearly clonal (because the groups do not differ much) then evolution by natural selection can not operate across the groups (remember, being clonal at the scale of the group does not mean there isn’t variation within groups, so selection still operates, just at a “lower” scale). But human culture is very different. Novel groups with their own distinctive cues can emerge very rapidly, and generate horizontal networks of affinity. Sometimes, as with accents, it is rather difficult for outsiders to a group to mimic and deceive because of a biologically “critical period” of enculturation (this might also be the role that radical body modification plays in a functional sense; it’s a difficult-to-fake identity marker, often irreversible).

That’s the theory. The main problem with these group-level models is that there’s always a lot of talk (theory), but a lot less empirical data. Hopefully that will change. The paper used a lot of experimental methods, and these are probably the way to go. Obviously you can’t put people in life or death situations, but you can at least discern general and specific patterns cross-culturally. And are these canned “games” any less valid than surveys to the WEIRD set?

Citation: Social networks and cooperation in hunter-gatherers, doi:10.1038/nature10736

Image credit: Wikipedia

January 16, 2012

The milkmen

Dienekes and Maju have both commented on a new paper which looked at the likelihood of lactase persistence in Neolithic remains from Spain, but I thought I would comment on it as well. The paper is: Low prevalence of lactase persistence in Neolithic South-West Europe. The location is on the fringes of the modern Basque country, while the time frame is ~3000 BC. Table 3 shows the major result:

Lactase persistence is a dominant trait. That means any individual with at least one copy of the T allele is persistent. As Maju noted a peculiarity here is that the genotypes are not in Hardy-Weinberg Equilibrium. Specifically, there are an excess of homozygotes. Using the SJAPL location as a potentially random mating scenario you should expect ~7 T/C genotypes, not 2. Interestingly the persistent individual in the Longar location also a homozygote.


HWE makes a few assumptions. For example, no selection, migration, mutation, or assortative mating. Deviation from HWE is suggestive of one of these dynamics. The sample size here is small, but the deviation is not to be dismissed. Recall that lactase persistence has dominant inheritance patterns. If the trait was being positively selected for you would only need one copy. The enrichment of homozygotes is unexpected if selection in situ is occurring here. It can not be ruled out that one is observing the admixture of two distinct populations. One generation of random mating would generate HWE, but when populations hybridize in realistic scenarios this is not always a plausible assumption. Rather, assortative mating often persists over the generations, slowing down the diminishing of population substructure.

Stepping back from speculation in this case what can we say? First, the LCT locus has a large mutational target. The trait of lactase persistence has arisen multiple times via different mutational events across the Old World. But, there does seem to be one particular variant which is found from Spain to Northern India. There is some circumstantial evidence that the allele had its origin somewhere in Central Eurasia, but currently its modal frequency is in Northern Europe, Scandinavia and Germany. The region in the genome around this mutation is characterized by a very long haplotype. It is one of the most definitive loci as a candidate for natural selection in the human genome. There is now a fair amount of ancient DNA evidence that lactase persistence in Europe is a feature of the last ~5,000 years or so. Among the modern Basques the frequency of the allele is 66 percent.

For me the key issue is teasing apart the role of migration and selection in each specific case. It does not seem to be correct that the frequency of the -13910T LCT allele in Basques and Punjabis is reflective of the frequency of recent common ancestry. That implies that natural selection is at work at this locus. On the other hand, the haplotype which is present in both the Basque and Punjabis is likely to be descended from a common set of individuals, implying that there is a genealogical chain connecting these two very distinct and distant Eurasian populations. Therefore, we can potentially make some inferences about the power of migration in spreading distinctive alleles. Often we partition selection from genealogical information, because selection so often serves to distort the signal. But the genealogical patterns may lay at the heart of the distribution of different natural selective events at the LCT locus.

Overall, I would say that the results from ancient DNA are disordering and clouding simple elegant models. One hopes and presumes that as sample sizes increase in this domain we’ll start to see more clarity as new paradigms crystallize.

Citation: European Journal of Human Genetics, 10.1038/ejhg.2011.254

January 5, 2012

James F. Crow, 1916-2012

Filed under: Evolution,Evolutionary Genetics,Genetics,James F. Crow — Razib Khan @ 2:01 am

Sad news. John Hawks passes along that James F. Crow has died. Further mention from the National Center For Science Education. A little over 5 years ago I sent Crow an email with only minimal expectation of response, asking about an interview. He responded in less than 24 hours! I think it says a lot about the man that he would respond to sincere questions out of the blue from basically a nobody. Here is his Wikipedia entry. And remember that Genetics has commissioned a series of retrospective essays in Crow’s honor.

December 27, 2011

The Genetical Theory of Natural Selection

I flog R. A. Fisher’s The Genetical Theory of Natural Selection a fair amount on this site. You don’t need to understand everything in the book, nor do you have to agree with everything in it, but it is a great point of departure toward understanding evolutionary genetics. I’ve noted that you can get it free in PDF format. But if you want to browse it online in a easier format, here you go:

(original link courtesy of Unz.org)

December 20, 2011

Out of Africa to Out of Arabia

Filed under: Evolution,Human Evolution — Razib Khan @ 3:13 pm

Dienekes and Greg Cochran have been talking about this possibility for a few years. But a combination of archaeological finds and the current unsettled nature of the human evolutionary genomics literature means that “Out of Arabia” is a real possibility (not laugh-out-loud crazy and weird). So I took the liberty of cooking up a new design for the RichardDawkins.net website. Science is about updating our prior assumptions, so it shouldn’t be too much of an issue. What I wonder: how would the population of the Kingdom of Saudi Arabia feel about replacing Ethiopia and Kenya in human evolution documentaries? Addendum: To be clear, this isn’t to say I accept “Out of Arabia” for the origin of most modern humans, including within Africa. Rather, I think it’s not a crazy idea anymore, especially in light of the weird results which imply that West Africans may be genetically closer to non-Africans than to Pygmies and San (and it would make more sense of older uniparental results which imply back-migration from Eurasia into Africa).

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