posted
Na, he knows better than that (I think). Right now, he is desperately scrambling through Keita's paper trying to find out a way to distort and say Keita did not say Dravidian samples shows shifts between Europe and Asia. Which then translates to Dravidians showing shifts between two major racial groups.
But of course he won't be able to distort, as the statements are clear as day.
Posts: 6572 | From: N.Y.C....Capital of the World | Registered: Jun 2008
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Sohini Ramachandran*†, Omkar Deshpande‡, Charles C. Roseman§, Noah A. Rosenberg¶, Marcus W. Feldman*, and L. Luca Cavalli-Sforza†
Abstract
Equilibrium models of isolation by distance predict an increase in genetic differentiation with geographic distance. Here we find a linear relationship between genetic and geographic distance in a worldwide sample of human populations, with major deviations from the fitted line explicable by admixture or extreme isolation. A close relationship is shown to exist between the correlation of geographic distance and genetic differentiation (as measured by FST) and the geographic pattern of heterozygosity across populations. Considering a worldwide set of geographic locations as possible sources of the human expansion, we find that heterozygosities in the globally distributed populations of the data set are best explained by an expansion originating in Africa and that no geographic origin outside of Africa accounts as well for the observed patterns of genetic diversity. Although the relationship between FST and geographic distance has been interpreted in the past as the result of an equilibrium model of drift and dispersal, simulation shows that the geographic pattern of heterozygosities in this data set is consistent with a model of a serial founder effect starting at a single origin. Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation.
Results
Testing whether a serial founder effect could give rise to the decay of expected heterozygosity with distance observed in Fig. 4A requires appropriate demographic models for calculating the effect of drift. We performed simulations of evolutionary processes to assess whether we could recover a similar pattern to what was computed from the data as shown in Fig. 4A (37). Assume for simplicity that we begin with a parental population, and there are n serial bottleneck episodes starting at the origin (the location of the parental population). In each bottleneck, a sample of individuals of size Nb founds the next colony, which is established at some distance from the previous colony and which remains isolated from all other colonies. This subsampling generates a succession of colonies in time, each of which grows to a large size K before generating the next colony in the chain. Each bottleneck episode decreases expected heterozygosity in the new colony by a factor of 1 1(2Nb) (39). To be precise, this computation includes the drift effect only of the first generation after the bottleneck. Based on this simple model of n bottlenecks with Nb founders at each bottleneck, an approximation for the total loss of expected heterozygosity from the beginning to the end of the expansion from the parental population due to the sequence of bottlenecks alone will be Regressing heterozygosity on distance from the parental colony, we can estimate Hby calculating the difference between the intercept of the regression line and the fitted value for the last population in the expansion (the furthest population from the origin). In Fig. 4A, the observed H is 0.12. Because n and Nb are unknown, Eq. 8 only allows the estimation of their ratio. Moreover, this simple model assumes no intermigration among colonies after their founding; it only accounts for genetic drift that occurs as a result of the bottlenecks in the serial founder effect, ignoring genetic drift (i) during the growth period where the founding population increases in size to carrying capacity and (ii) while the population stays at carrying capacity as the subsequent colonies are formed. These components will increase the amount of drift experienced by populations over that which would ensue from a population of constant size K. Simulation enables the evaluation of these components of the evolutionary process by using estimable quantities, such as the mutation rate of microsatellites and the sizes of populations (see Supporting Text, which is published as supporting information on the PNAS web site, for more discussion). Fig. 4B shows that simulation can produce heterozygosity values similar to those observed in the data set, giving a simulated value for H of 0.12, very close to the observed value. Hsim will differ from H˜ in Eq. 8 (see Supporting Text). The main assumption in the simulation (Fig. 4B) is that Nb, the number of founders at each bottleneck, is of the order of a hunter–gatherer tribe (35, 36).
Discussion
Geographic distance is a good predictor of genetic distance on a global scale (Fig. 1). The pattern’s robustness is indicated by our ability to reasonably explain anomalies (Fig. 2) based on what is generally believed to have occurred during the past 100,000 years of modern human history (29). We also find a close relationship between the correlation of FST and geographic distance (Fig. 1) and the geographic pattern of heterozygosity across populations (Fig. 4A). An increase in genetic distance with geographic distance has been observed in the past and has been attributed to equilibrium models of isolation by distance, but simulation results show that the geographic pattern of heterozygosities in the HGDP-CEPH populations is consistent with a serial founder effect starting at a single origin. Further, the observed pattern of within-population diversity is best explained by an origin in Africa (Fig. 5). By studying the relationship between genetic and geographic distance, we can assess the relative importance of genetic drift and natural selection in determining the genetic variation observed among human populations. The average contribution of drift generated by the serial founder effect might be estimated from the properties of the regression in Figs. 1B and 4A. Because our regressions explain 76–78% of the observed genetic variation, this quantity is therefore an estimate of the minimum influence that drift, due to the serial founder effect, has on the total variation observed. In other words, the fraction of the variation in heterozygosity across human populations that is explained by drift is at least 76–78%. If stabilizing selection has been a major force in human evolution, then the decrease of average heterozygosity would be reduced, and the slope in Fig. 4A would be less negative (by an unknown amount). The residual 22–24% of genetic variation not explained by the regression is generated by population-specific selection, drift, and mutational histories. The deviation from the regression of each individual population (Fig. 4A) or of each population pair (Fig. 2) is a consequence of each population’s particular demographic history (40). But it is clear that part of these deviations also may be due to different selective conditions met by these populations in the different environments to which they have been exposed. Therefore, we estimate that 76–78% can be considered a lower bound on the effect of drift, and 22–24% an upper bound on the effect of selection, in the genetic differentiation of human populations.Posts: 6572 | From: N.Y.C....Capital of the World | Registered: Jun 2008
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posted
From above, a rather well exampled elaboration on the effects of population bottlenecks and result thereof....
quote:Assume for simplicity that we begin with a parental population, and there are n serial bottleneck episodes starting at the origin (the location of the parental population). In each bottleneck, a sample of individuals of size Nb founds the next colony, which is established at some distance from the previous colony and which remains isolated from all other colonies. This subsampling generates a succession of colonies in time, each of which grows to a large size K before generating the next colony in the chain. Each bottleneck episode decreases expected heterozygosity in the new colony by a factor of 1 1(2Nb) (39). To be precise, this computation includes the drift effect only of the first generation after the bottleneck. Based on this simple model of n bottlenecks with Nb founders at each bottleneck, an approximation for the total loss of expected heterozygosity from the beginning to the end of the expansion from the parental population due to the sequence of bottlenecks alone will be Regressing heterozygosity on distance from the parental colony, we can estimate Hby calculating the difference between the intercept of the regression line and the fitted value for the last population in the expansion (the furthest population from the origin). In Fig. 4A, the observed H is 0.12. Because n and Nb are unknown, Eq. 8 only allows the estimation of their ratio. Moreover, this simple model assumes no intermigration among colonies after their founding; it only accounts for genetic drift that occurs as a result of the bottlenecks in the serial founder effect, ignoring genetic drift (i) during the growth period where the founding population increases in size to carrying capacity and (ii) while the population stays at carrying capacity as the subsequent colonies are formed. These components will increase the amount of drift experienced by populations over that which would ensue from a population of constant size K.
Posts: 6572 | From: N.Y.C....Capital of the World | Registered: Jun 2008
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quote:Geographic distance is a good predictor of genetic distance on a global scale (Fig. 1). The pattern’s robustness is indicated by our ability to reasonably explain anomalies (Fig. 2) based on what is generally believed to have occurred during the past 100,000 years of modern human history (29). We also find a close relationship between the correlation of FST and geographic distance (Fig. 1) and the geographic pattern of heterozygosity across populations (Fig. 4A). An increase in genetic distance with geographic distance has been observed in the past and has been attributed to equilibrium models of isolation by distance, but simulation results show that the geographic pattern of heterozygosities in the HGDP-CEPH populations is consistent with a serial founder effect starting at a single origin.
Posts: 6572 | From: N.Y.C....Capital of the World | Registered: Jun 2008
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posted
^Interesting additions. From a DNA phylogenetic standpoint, as heterozygosity increases, linkage disequilibrium tends to decrease; and vice versa, as heterozygosity decreases in a dataset, chances are the same dataset will be marked by greater linkage disequilibrium. African samples generally tend to sport more heterozygosity; the authors in the following, for example, saw this as well:
Global Haplotype Diversity in the Human Insulin Gene Region John D.H. Stead1,3,4, Matthew E. Hurles2 and Alec J. Jeffreys1
The insulin minisatellite (INS VNTR) has been intensively analyzed due to its associations with diseases including diabetes. We have previously used patterns of variant repeat distribution in the minisatellite to demonstrate that genetic diversity is unusually great in Africans compared to non-Africans. Here we analyzed variation at 56 single nucleotide polymorphisms (SNPs) flanking the minisatellite in individuals from six populations, and we show that over 40% of the total genetic variance near the minisatellite is due to differences between Africans and non-Africans, far higher than seen in most genomic regions and consistent with differential selection acting on the insulin gene region, most likely in the non-African ancestral population. Linkage disequilibrium was lower in African populations, with evidence of clustering of historical recombination events. Analysis of haplotypes from the relatively nonrecombining region around the minisatellite revealed a star-shaped phylogeny with lineages radiating from an ancestral African-specific haplotype. These haplotypes confirmed that minisatellite lineages defined by variant repeat distributions are monophyletic in origin. These analyses provide a framework for a cladistic approach to future disease association studies of the insulin region within both African and non-African populations, and they identify SNPs which can be rapidly analyzed as surrogate markers for minisatellite lineage.
The insulin minisatellite, located within the promoter of the human insulin gene, has been intensely investigated for nearly two decades due to its associations with diseases such as diabetes (Bell et al. 1984; Bennett and Todd 1996). Most studies have analyzed populations of European descent where low diversity at the minisatellite combined with strong linkage disequilibria in flanking regions make it difficult to distinguish between etiological and associated variants (Bennett and Todd 1996; Doria et al. 1996). The identification of etiological polymorphisms in the insulin region may therefore require analysis of a range of different populations, in particular those showing a greater range of haplotype diversity than that seen in Europeans...
Franck Prugnolle1, Andrea Manica2 and François Balloux1
A leading theory for the origin of modern humans, the ‘recent African origin’ (RAO) model [1], postulates that the ancestors of all modern humans originated in East Africa and that, around 100,000 years ago, some modern humans left the African continent and subsequently colonised the entire world, displacing previously established human species such as Neanderthals in Europe [2,3]. This scenario is supported by the observation that human populations from Africa are genetically the most diverse [2] and that the genetic diversity of non-African populations is negatively correlated with their genetic differentiation towards populations from Africa [3]. Here we add further compelling evidence supporting the RAO model by showing that geographic distance — not genetic distance as in [3] — from East Africa along likely colonisation routes is an excellent predictor for genetic diversity of human populations (R2 = 85%). Our results point to a history of colonisation of the world characterised by a very large number of small bottlenecks [4] and limited subsequent gene flow. The pattern of decrease in genetic diversity along colonisation routes is very smooth and does not provide evidence for major genetic discontinuities that could be interpreted as evidence for human ‘races’ [2,5].Posts: 6572 | From: N.Y.C....Capital of the World | Registered: Jun 2008
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posted
^ Yet Assopen chooses to stalk me in every other thread other than the ones that really count to him like this one...
Assopen just begs me and pleads me to screw him, but again I'm not one of his boy-lovers.
If he wants to get screwed here again, just present him the FACTS as usual. Posts: 26322 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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posted
^ Why are you constantly interrupting the flow of the thread with talk of men screwing?
Doug posted some great photos which I was digging only to yet again see you posting your deviate thoughts, as if a Robot could screw man or woman. I have no desire to form the picture in mind of a Robot performing homosexual acts with a human male. Please stop, or better yet, Please take horrible vision to one of Egmond's threads where it will be appreciated.
Posts: 3595 | From: Moved To Mars. Waiting with shotgun | Registered: Dec 2006
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posted
^ Sorry but I am merely addressing a sour member of the Aprasscee gang that the fag who keeps stalking me belongs to.
I'm not a homosexual, neither do I have anything against homosexuals.
But since I wasn't even addressing you I don't know why you seemed so vexed unless the such talk 'touches' you deeply so to speak.
Posts: 26322 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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posted
I see there are no replies from the ass in threads like this that really matter. Yet the ass chooses to make his issue pertaining to this topic in other threads and worse-- stalk me like the deranged schoolgirl he identifies with in his mind...
Posts: 26322 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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wished there were actual moderators to delete the few posts which have no pertinence to the topic on this thread, but hey, for those reading can learn something...
Topic: Distance from Africa, not climate, explains within-population phenotypic diversityPosts: 6572 | From: N.Y.C....Capital of the World | Registered: Jun 2008
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