Saturday, August 18, 2007

Evolution, a story told by the winners   posted by David Boxenhorn @ 8/18/2007 09:54:00 PM

I had what I seemed to me like an interesting thought when I read this, and I wanted to explore it further. But I have been very busy these days, and I just don't have the spare cycles, so I'm just going to throw it out there. My biggest question is: "What am I missing?" R. A. Fisher didn't think that epistasis was an important evolutionary force. I can't believe he would miss this, so the only alternative is that he considered it...

From the link:

Finally, that we failed to find a significant grandfather effect in our monogamous society in which we restricted our data to those men who married only once in their lifetimes (and hence could only gain fitness by grandfathering after the menopause of their wife) strongly suggests that the evolution of prolonged life in men cannot be explained by the selective benefits of grandfathering.

My thought, as I expressed in the comments of that post, was that average fitness is not particularly meaningful, since a relatively small number of males at the top of the social pyramid probably had a disproportionate evolutionary impact - what really counts is the grandfather effect among them. I can easily imagine a scenario where grandfathers decrease fertility of ordinary families (another mouth to feed...), but increase it among the rich. The long-term fitness impact of grandfathers could well be positive, even though the average impact is negative, since the rich have the biggest long-term evolutionary impact.

I can tell this same story on the gene level. Imagine a population which is 99% "aabb" and 1% "aabB", each of which have equal fitness. Now, imagine that there's a mutation "A" that reduces fitness by 10% in "bb" individuals, but raises fitness by 10% in "bB" individuals. Let's say by chance we get a "aAbB" individual before the "A" allele dies out. That "aAbB" individual will have the same fitness as a normal "aabb" individual, since its offspring will be 25% "aabb" (average fitness), 25% "aAbb" (10% lowered fitness), 25% "aAbB" (10% higher fitness), and 25% "aabB" (average fitness). Nevertheless, over time, the "A" allele will increase and eventually fix (together with the "B" allele). (Those of you who want to quibble about the percentages can adjust them accordingly.)

Now that seems like an interesting result to me! We talk a lot about average fitness here, but if I am not mistaken, average fitness can tell a story that's very different from what's really going on. Increasing the fitness of winners seems to count a lot more than decreasing the fitness of losers - and in evolution it's the winner's story that will eventually be told.

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Friday, August 03, 2007

Convergent evolution of lactase persistence - part n   posted by Razib @ 8/03/2007 02:40:00 PM

Note: I got this article via AJHG's RSS. It doesn't seem to have gone live on the site so there might be temporary problems accessing the link.

Evidence of Still-Ongoing Convergence Evolution of the Lactase Persistence T-13910 Alleles in Humans:
A single-nucleotide variant, C/T-13910, located 14 kb upstream of the lactase gene (LCT), has been shown to be completely correlated with lactase persistence (LP) in northern Europeans. Here, we analyzed the background of the alleles carrying the critical variant in 1,611 DNA samples from 37 populations. Our data show that the T-13910 variant is found on two different, highly divergent haplotype backgrounds in the global populations. The first is the most common LP haplotype (LP H98) present in all populations analyzed, whereas the others (LP H8-H12), which originate from the same ancestral allelic haplotype, are found in geographically restricted populations living west of the Urals and north of the Caucasus. The global distribution pattern of LP T-13910 H98 supports the Caucasian origin of this allele. Age estimates based on different mathematical models show that the common LP T-13910 H98 allele (~5,000-12,000 years old) is relatively older than the other geographically restricted LP alleles (~1,400-3,000 years old). Our data about global allelic haplotypes of the lactose-tolerance variant imply that the T-13910 allele has been independently introduced more than once and that there is a still-ongoing process of convergent evolution of the LP alleles in humans.

Two things to note

1) A recent common origin for much of the Eurasian lactase persistence phenotype is interesting. The period between 5 and 12 thousand years ago was obviously very significant and an inflection point in many ways in terms of the history of our species. Surveys of neutral markers which are supposedly reasonable proxies for ancestry imply that we should be cautious about mass population replacements across Eurasia. For example, it seems likely that the majority of Europeans and South Asians are descended from lineages already extant within their current geographic bounds at the end of the last Ice Age (though more or less significant impacted by population waves of advance triggered by the Neolithic revolution in the Middle East). Nevertheless, some biologists have argued that the sweeping action across demes of mutations of large effect are powerful enough to maintain species continuity and drive broad phenotypic convergences. One can conceptualize the genetic dynamics at work as a broad substrate of ancestrally informative alleles clustered across Eurasia, but tightly laced together by synchronous sweeps and pulses of functionally salient genes.

2) The newer, localized, LP variants are intriguing. The time window is very narrow here. Evolutionary theory tells us that in reaction to a strong selective force phenotypic change may immediately be affected by mutations of large effect. These mutants may be good at what they are meant to do, but also have negative side effects. Over time various selection pressures will reshape the genetic architecture with a host of modifiers and smaller effect mutants which result in a population subject to less stress via correlated responses due to the initial mutant of large effect. I wonder if the newer variants are signals that the genetic background is still working to optimize adaptation to a high lactose diet.

Related: See here and here.

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Monday, June 25, 2007

Nick Wade on recent evolution human   posted by Razib @ 6/25/2007 08:43:00 PM

Humans Have Spread Globally, and Evolved Locally:
No one yet knows to what extent natural selection for local conditions may have forced the populations on each continent down different evolutionary tracks. But those tracks could turn out to be somewhat parallel. At least some of the evolutionary changes now emerging have clearly been convergent, meaning that natural selection has made use of the different mutations available in each population to accomplish the same adaptation.

This is the case with lactose tolerance in European and African peoples and with pale skin in East Asians and Europeans.

Nothing new to readers of this weblog, but Wade does a good job surveying the various angles.

Related articles on recent human evolution.

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Monday, June 18, 2007

More detecting natural selection   posted by Razib @ 6/18/2007 04:03:00 PM

A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
The evolution of new functions and adaptation to new environments occurs by positive selection, whereby beneficial mutations increase in frequency and eventually become fixed in a population. Detecting such selection in humans is crucial for understanding the importance of past genetic adaptations and their role in contemporary common diseases. Methods have already been developed for detecting the signature of positive selection in large, genome-scale datasets (such as the “HapMap”). Positive selection is expected to more rapidly increase the frequency of an allele, and hence, the length of the haplotype (extent of DNA segment) associated with the selected allele, relative to those that are not under selection. Such methods compare haplotype lengths within a single population. Here, we introduce a new method that compares the lengths of haplotypes associated with the same allele in different populations. We demonstrate that our method has greater power to detect selective sweeps that are fixed or nearly so, and we construct a statistical framework that shows that our method reliably detects positive selection. We applied our method to the HapMap data and identified approximately 500 candidate regions in the human genome that show a signature of recent positive selection. Further targeted studies of these regions should reveal important genetic adaptations in our past.

I'm in a hurry/busy, so no real comment. It's PLOS, so it's free. Read it.

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Etruscans - don't know nothing about DNA   posted by Razib @ 6/18/2007 12:00:00 PM

The Etruscan origin story is now in the news again after the lead researcher presented his findings that these ancient people show strong evidence of a genetic affinity with Anatolians at a conference. I put a quick round up over at ScienceBlogs, but this piece in the LA Times is a bit disconcerting. Here are some archaeologists:
"I guess I would have to say that I am unconvinced at this stage," said archeologist Anthony Tuck of the University of Massachusetts at Amherst, who is excavating an Etruscan site in Italy. "It is premature to declare the issue resolved on our current understanding of this genetic evidence."

Archeologist Jean Macintosh Turfa of the University of Pennsylvania's Museum of Archeology and Anthropology was more dismissive. "There is really no sound archeological evidence that shows the influx of a big migration, or any kind of influx, from Asia Minor," she said. "There is never a sharp break in cultures, no destroyed villages, etcetera."

Turfa and Tuck hold to the view that the Etruscans evolved from the Villanovan culture, which emerged in central Italy. But the genetic findings will force a harder look at the evidence about their origins.

I really hope that the reporter didn't go quote mining until he found someone with a "dissenting" view, that's just bad journalism. Let's review the lines of evidence:

1) Y chromosomal lineages suggest a link with Anatolians.

2) mtDNA, both ancient and modern, suggest a link with Anatolians. The ancient mtDNA results (from 2004) was argued by some to have been possible contamination, etc., but I think that the findings from modern mtDNA (combined with other data) should force us to reorient our priors in evaluating that previous finding.

3) mtDNA from cattle suggests a parallel phylogenetic relationship between Anatolian and Tuscan populations.

These genetic arrows are now converging upon one conclusion: that there was some link between ancient Anatolians and Etruscans beyond what we would expect. One could dismiss one or two findings, but the alignment here should be worth noting. But that's not all. The island of Lemnos yields evidence that a language closely related to Etruscan before the Athenian conquest of the 6th century BCE was in use. Lemnos is the north Aegean. One plausible explanation is that an Etruscan trading colony was long resident here. Another explanation is that the inhabitants of Lemnos are part of the same "Lydian" Diaspora as the Etruscans. The Etruscans-are-native-to-Italy hypothesis would imply that the former explanation is what we should accept, but in light of the new data the Lemnos records should, I think, be taken as evidence of the latter scenario. The ancient scholars who addressed the origin of the Etruscans offered three alternative scenarios, that they were indigenous to Italy, that they were from Anatolia, or that they were from northern Europe. What is the likelihood that out of the sample space of possibilities Anatolia (as opposed to Greece, Libya, Egypt, etc.) would be selected as a possible point of origin? Prior to the emergence of these strong genetic data I do think one could imagine it was a flight of fantasy, but now it seems likely that its selection was not arbitrary.

The genetic data seems strong to me. That being said, the archaeologists have long noted continuities between the Villanovan Culture and the Etruscans. What gives? I think the solution is simple: the Etruscans had a non-trivial (genetically detectable to the present) exogenous element, but it also drew upon the local substrate. Taking a step outside of this particular issue that should be pretty clear & obvious. The Greeks show this hybrid tendency, a large proportion of words in their language show no Indo-European cognates. There are legends of Pelasgians, a confused term which might have referred to unassimilated elements amongst the non-Greek speaking inhabitants of the peninsula. The same dynamic can be seen in north India, where a hybrid culture arose which exhibited both pre-Aryan and Aryan elements. The archaeological continuity might very well be a reality in Tuscany simply because that the Etruscans did not exterminate the local peasantry, but rather, entered into a relationship of overlordship and subsequent cultural absorption. The continuity of material culture might be due to the fact that the folkways of Anatolia (housing structure and material, field arrangments, crops, etc.) were not applicable to the ecological needs of north-central Italy, or that the original settler Etruscans were a particular occupational slice of their peoples, perhaps a mercantile elite who were oriented toward the sea (they were well known traders) as opposed to agriculture. Just as Christian peasants and landlords in Anatolia were absorbed into the culture and identity of their Turkic rulers after 1100 over a period of time, so it seems that a possible model is one where Etruscan elite culture had this pull upon locals whom they ruled. Subjects of the Roman Empire absorbed some elements of Romanitas from their culture elites (language and religion), but they did not all become the villagers of Latium in replica form simply due to the local ecological constraints (dwelling architecture and farming techniques suitable for the Mediterranean don't transplant that well to northern Gaul). New data forces us to construct amenable hypotheses, not simply dismiss it.

Note: I put Lydian in quotes because it is likely an anachronism. The Etruscans were as Lydian as the tribes who resided on the north shore of lake Superior in 1500 were "Canadian."

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Wednesday, June 13, 2007

Why genes don't determine race?   posted by Razib @ 6/13/2007 10:59:00 AM

TNR, the journal of the center-left, just published an article titled Why genes don't determine race. The article doesn't merit much of a response aside from "Why Platonism is wrong on race." The article makes it implicitly clear that the new racial genetics is often one of conditional probabilities, not fixed determinism, but the strawman of "genetic determinism" shines brightly in the rhetoric. In any case, there are good points made in the piece, the obesity epidemic that is rampant in the black American population isn't going to be solved by declarations that it is "in their genes." But, an understanding of the genetic background adds non-trivial utility to formulating a proper public policy response, because there are likely some issues of norm of reaction lurking in the background. As documented in Some Like it Hot: Food, Genes and Cultural Diversity, varied populations often exhibit different nutritional responses.

Addendum: In the annals of race, Slow Wave Activity During Sleep Is Lower In African-Americans Than Caucasians.

Related: Race the current consensus. The Platonic Ideal and the Empirical Reality. Race is obsolete...? Reality of race is one place. Race.

Update: This response very good.