Tag: Natural Selection

The end of genomics, the beginning of analysis

By Razib Khan | September 11, 2013 12:26 am

A Tree of Life

Evolutionary processes which play out across the tree of life are subject to distinct dynamics which can shape and influence the structure and characteristics of individuals, populations, and whole ecosystems. For example, imagine the phylogeny and population genetic characteristics of organisms which are endemic to the islands of Hawaii. Because the Hawaiian islands are an isolated archipelago the expectation is that lineages native to the region are going to be less shaped by the parameter of migration, or gene flow between distinct populations, than might otherwise be the case. Additionally, presumably there was a “founding” event of these endemic Hawaiian lineages at some distant point in the past, so another expectation is that most of the populations would exhibit evidence of having gone through a genetic bottleneck, where the power of random drift was sharply increased for several generations. The various characteristics, or states, which we see in the present in an individual, population, or set of populations, are the outcome of a long historical process, a sequence of precise events. To understand evolution properly it behooves us to attempt to infer the nature and magnitude of these distinct dynamic parameters which have shaped the tree of life.

Credit: Verisimilus

For many the image of evolutionary processes brings to mind something on a macro scale. Perhaps that of the changing nature of protean life on earth writ large, depicted on a broad canvas such as in David Attenborough’s majestic documentaries over millions of years and across geological scales. But one can also reduce the phenomenon to a finer-grain on a concrete level, as in specific DNA molecules. Or, transform it into a more abstract rendering manipulable by algebra, such as trajectories of allele frequencies over generations. Both of these reductions emphasize the genetic aspect of natural history.

Credit: Johnuniq

Obviously evolutionary processes are not just fundamentally the flux of genetic elements, but genes are crucial to the phenomena in a biological sense. It therefore stands to reason that if we look at patterns of variation within the genome we will be able to infer in some deep fashion the manner in which life on earth has evolved, and conclude something more general about the nature of biological evolution. These are not trivial affairs; it is not surprising that philosophy-of-biology is often caricatured as philosophy-of-evolution. One might dispute the characterization, but it can not be denied that some would contend that evolutionary processes in some way allow us to understand the nature of Being, rather than just how we came into being (Creationists depict evolution  as a religion-like cult, which imparts the general flavor of some of the meta-science and philosophy which serves as intellectual subtext).

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Sexual selection: ignore the blonde?

By Razib Khan | June 23, 2013 2:56 pm

Frank analytic clarity?

Sexual selection is a big deal. A few years ago Geoffrey Miller wrote The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature, which seemed to herald a renaissance of the public awareness of this evolutionary phenomenon, triggered in part by debates over Amotz Zahavi’s Handicap Principle in the 1970s. Of course Charles Darwin discussed the process in the 19th century, and it has always been part of the arsenal of the evolutionary biologist (I first encountered it in Jared Diamond’s The Third Chimpanzee, where he lent some credence to Darwin’s supposition that human racial differences may be a consequence of sexual selection). But this bump in recognition for sexual selection seems to be accompanied by its co-option as a deus ex machina for all sorts of unexplained events. And yet as they say, that which explains everything explains nothing.

To get a better sense of the current scientific  literature I consulted A Guide to Sexual Selection Theory in the Annual Review of Ecology, Evolution, and Systematics. The image above is from an actual box in this review! Normally technical boxes illuminate with an air of superior authority (e.g. “it therefore follows from eq. 1…/”), but it seems to me that the admission that a parameter can be represented by the verbal assertion that it’s complicated tells us something about the state of sexual selection theory. In short: its formal basis is baroque because the dynamic itself is not amenable to easy decomposition.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics

How Chinese genetics is like Chinese food

By Razib Khan | July 27, 2011 3:46 pm

Representatives of Szechuan and Shangdong cuisine


The Pith: The Han Chinese are genetically diverse, due to geographic scale of range, hybridization with other populations, and possibly local adaptation.

In the USA we often speak of “Chinese food.” This is rather peculiar because there isn’t any generic “Chinese cuisine.” Rather, there are regional cuisines, which share a broad family similarity. Similarly, American “Mexican food” and “Indian food” also have no true equivalent in Mexico or India (naturally the novel American culinary concoctions often exhibit biases in the regions from which they sample due to our preferences and connections; non-vegetarian Punjabi elements dominate over Udupi, while much authentic Mexican American food has a bias toward the northern states of that nation). But to a first approximation there is some sense in speaking of a general class of cuisine which exhibits a lot of internal structure and variation, so long as one understands that there is an important finer grain of categorization.

Some of the same applies to genetic categorizations. Consider two of the populations in the original HapMap, the Yoruba from Nigeria, and the Chinese from Beijing. There are ~30 million Yoruba, but over 1 billion Han Chinese! Even granting that the Yoruba seem excellent representatives of Sub-Saharan African genetic variation (not Bantu, but not far from the Bantu), there are still more Han Chinese than Sub-Saharan Africans (including the African Diaspora). So it’s nice that over the past few years there’s been a deep-dive into Han genetics. A new paper in the European Journal of Human Genetics focuses on the north-south difference among Han Chinese, using groups flanking them to their north and south as references, Natural positive selection and north–south genetic diversity in East Asia.

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"What if you're wrong" – haplogroup J

By Razib Khan | June 28, 2011 2:52 pm

Back when this sort of thing was cutting edge mtDNA haplogroup J was a pretty big deal. This was the haplogroup often associated with the demic diffusion of Middle Eastern farmers into Europe. This was the “Jasmine” clade in Seven Daughters of Eve. A new paper in PLoS ONE makes an audacious claim: that J is not a lineage which underwent recent demographic expansion, but rather one which has been subject to a specific set of evolutionary dynamics which have skewed the interpretations due to a false “molecular clock” assumption. By this assumption, I mean that mtDNA, which is passed down in an unbroken chain from mother to daughter, is by and large neutral to forces like natural selection and subject to a constant mutational rate which can serve as a calibration clock to the last common ancestor between two different lineages. Additionally, mtDNA has a high mutational rate, so it accumulates lots of variation to sample, and, it is copious, so easy to extract. What’s not to like?

First, the paper, Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe:

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Convergent evolution happens!

By Razib Khan | June 20, 2011 4:04 am

In the image to the left you see three human males. You can generate three pairings of these individuals. When comparing these pairs which would you presume are more closely related than the other pairs? Now let me give you some more information. The rightmost image is of the president of Tanzania. The middle image is of the president of Taiwan (Republic of China). And finally, the leftmost image is of the prime minister of Papua New Guinea. With this information you should now know with certainty that the prime minister of Papua New Guinea and the president of Taiwan are much more closely related than either are to the president of Tanzania. But some of you may not have guessed that initially. Why? I suspect that physical inspection may have misled you. One of the most salient visible human characteristics is of the complexion of our largest organ, the skin. Its prominence naturally leads many to mistakenly infer relationships where they do not exist.

This was certainly an issue when European explorers encountered the peoples of Melanesia. An older term for Melanesians is “Oceanic Negro,” and some sources suggest that the Spaniards who named the island New Guinea did so with an eye to the old Guinea on the coast of West Africa. To the left is an unrooted tree which illustrates the relationships between Papuans, Bantu from Kenya, and Han Chinese. Since the font is small I’ve underlined the focal populations in red. Africans are always the “outgroup” to any two non-African populations. This is a robust pattern whenever you look at averaged total genome phylogenies. In other words, when you don’t privilege particular genes in a phylogeny humanity can be divided into African and non-African branches.

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The evolutionary effect of the sky gods

By Razib Khan | April 24, 2011 4:02 pm

ResearchBlogging.orgLast week I reviewed ideas about the effect of “exogenous shocks” to an ecosystem of creatures, and how it might reshape their evolutionary trajectory. These sorts of issues are well known in their generality. They have implications from the broadest macroscale systematics to microevolutionary process. The shocks point to changes over time which have a general effect, but what about exogenous parameters which shift spatially and regularly? I’m talking latitudes here. The further you get from the equator the more the climate varies over the season, and the lower the mean temperature, and, the less the aggregate radiation the biosphere catches. Allen’s rule and Bergmann’s rule are two observational trends which biologists have long observed in relation to many organisms. The equatorial variants are slimmer in their physique, while the polar ones are stockier. Additionally, there tends to be an increase in mean mass as one moves away from the equator.

But these rules are just general observations. What process underlies these observations? The likely culprit would be natural selection of course. But the specific manner in which this process shakes out, on both the organismic and genetic level, still needs to be elucidated in further detail. A new paper in PLoS Genetics attempts to do this more rigorously and deeply than has been done before for one particular world wide mammalian species, H. sapiens sapiens. We have spanned the latitudes and longitudes, and so we’re a perfect test case for an exploration of the broader microevolutionary forces which shape variation.

The paper is Adaptations to Climate-Mediated Selective Pressures in Humans. Its technical guts can be intimidating, but its initial questions and final answers are less daunting. So let’s jump straight to the last paragraph of the discussion:

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Body odor, Asians, and earwax

By Razib Khan | October 25, 2010 3:36 am

EarWhen I was in college I would sometimes have late night conversations with the guys in my dorm, and the discussion would random-walk in very strange directions. During one of these quasi-salons a friend whose parents were from Korea expressed some surprise and disgust at the idea of wet earwax. It turns out he had not been aware of the fact that the majority of the people in the world have wet, sticky, earwax. I’d stumbled onto that datum in the course of my reading, and had to explain to most of the discussants that East Asians generally have dry earwax, while convincing my Korean American friend that wet earwax was not something that was totally abnormal. Earwax isn’t something we explore in polite conversation, so it makes sense that most people would be ignorant of the fact that there was inter-population variation on this phenotype.

But it doesn’t end there. Over the past five years the genetics of earwax has come back into the spotlight, because of its variation and what it can tell us about the history and evolution of humans since the Out of Africa event. Not only that, it seems the variation in earwax has some other phenotypic correlates. The SNPs in and around ABCC11 are a set where East Asians in particular show signs of being different from other world populations. The variants which are nearly fixed in East Asia around this locus are nearly disjoint in frequency with those in Africa. Here are the frequencies of the alleles of rs17822931 on ABCC11 from ALFRED:
abcc11A

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Chosen genes of the Chosen People

By Razib Khan | August 27, 2010 1:48 am

ashjewheadshotLast spring two very thorough papers came out which surveyed the genetic landscape of the Jewish people (my posts, Genetics & the Jews it’s still complicated, Genetics & the Jews). The novelty of the results was due to the fact that the research groups actually looked across the very diverse populations of the Diaspora, from Morocco, Eastern Europe, Ethiopia, to Iran. They constructed a broader framework in which we can understand how these populations came to be, and how they relate to each other. Additionally, they allow us to have more perspective as to the generalizability of medical genetics findings in the area of “Jewish diseases,” which for various reasons usually are actually findings for Ashkenazi Jews (the overwhelming majority of Jews outside of Israel, but only about half of Israeli Jews).

Just as the two aforementioned papers were deep explorations of the genetic history of the Jewish people, and allowed for a systematic understanding of their current relationships, a new paper in PNAS takes a slightly different tack. First, it zooms in on Ashkenazi Jews. The Jews whose ancestors are from the broad swath of Central Europe, and later expanded into Poland-Lithuania and Russia. The descendants of Litvaks, Galicians, and the assimilated Jewish minorities such as the Germans Jews. Second, though constrained to a narrower population set, the researchers put more of an emphasis on the evolutionary parameter of natural selection. Like any population Jews have been impacted by drift, selection, migration (and its variant admixture), and mutation. Teasing apart these disparate parameters may aid in understanding the origin of Jewish diseases.

ResearchBlogging.orgThe paper is open access, so you don’t have to take my interpretation as the last word. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population:

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CATEGORIZED UNDER: Anthroplogy, Genetics

Disease as a byproduct of adaptation

By Razib Khan | July 22, 2010 12:34 am

How we perceive nature and describe its shape are a matter of values and preferences. Nature does not take notice of our distinctions; they exist only as instruments which aid in our comprehension. I’ve brought this up in relation to issues such as categorization of recessive vs. dominant traits. The offspring of people of Sub-Saharan African and non-African ancestry where the non-African parent has straight or wavy hair tend to have very curly hair. Therefore, one may say that the tightly curled hair form is dominant to straight or wavy hair. But, it is also the case that there is some modification in relation to the African parent in the offspring, so the dominance is not complete. When examining the morphology of the follicle, which determines the extent of the hair’s curl, the offspring may in fact exhibit some differences from both parents. In other words our perception of the outcomes of inheritance are contingent to some extent on our categorization of the traits as well as our specific focus along the developmental pathway.

Or consider the division between “traits” and “diseases.” The quotations are necessary. Lactose intolerance is probably one of the best cases to illustrate the gnarly normative obstructions which warp our perceptions. As a point of fact lactose intolerance is the ancestral human state, and numerically predominant. It is the “wild type.” Lactose tolerance is a relatively recent adaptation, found among a variety of West Eurasian and African populations. A more politically correct term, lactase persistence, probably better encapsulates the evolutionary history of the trait, which has shifted from the class of disease to that of genetic trait when we evaluate the bigger picture (obviously diseases are simply “bad” traits”).

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More on recombination & natural selection

By Razib Khan | March 28, 2010 1:31 pm

A follow up to the post below, see John Hawks, Selection’s genome-wide effect on population differentiation and p-ter’s Natural selection and recombination. As I said, it’s a dense paper, and I didn’t touch on many issues.

CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics, Science
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