posted
A recap about the immense genetic and phenotypic diversity in Africa which is overwhelmingly more diverse than it is outside of Africa.....
quote:Originally posted by The Explorer: Distance from Africa, not climate, explains within-population phenotypic diversity in humans
Lia Betti1, François Balloux2, William Amos1, Tsunehiko Hanihara3, Andrea Manica1
December 02, 2008
Abstract
The relative importance of ancient demography and climate in determining worldwide patterns of human within-population phenotypic diversity is still open to debate. Several morphometric traits have been argued to be under selection by climatic factors, but it is unclear whether climate affects the global decline in morphological diversity with increasing geographical distance from sub-Saharan Africa. Using a large database of male and female skull measurements, we apply an explicit framework to quantify the relative role of climate and distance from Africa. We show that distance from sub-Saharan Africa is the sole determinant of human within-population phenotypic diversity, while climate plays no role. By selecting the most informative set of traits, it was possible to explain over half of the worldwide variation in phenotypic diversity. These results mirror those previously obtained for genetic markers and show that ‘bones and molecules’ are in perfect agreement for humans.
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Of course, climate, environment, living conditions, random mutation and genetic drift, and globalization [inter-ethnic miscegenation as a consequence of immigration] chime in in varying forms and in complex ways in influencing cranio-morphometric variation, as I've noted here before, but what these folks seem to be observing, at least from the little mentioned in the abstract above, is more diversity in Africa, especially sub-Saharan Africa, vs. that elsewhere. It goes back to that old age basic lesson: non-African groups derived from a subset of Africans, and hence, loss of diversity or a fraction of diversity. Though variations would occur in OOA, as a result of a number of bottleneck events and elements of the aforementioned factors, the overall diversity within the population is very likely to be impacted by that of the "founding" population, notwithstanding subsequent expansion events. The pre-existing variation in the original OOA subgroups was already a fraction of that in the African homeland, and there is reason to suspect that a series of bottlenecks events, that marked the dispersal of OOA migrants, would have led to further losses in diversity along the way.
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quote: but what these folks seem to be observing, at least from the little mentioned in the abstract above, is more diversity in Africa, especially sub-Saharan Africa, vs. that elsewhere. It goes back to that old age basic lesson: non-African groups derived from a subset of Africans, and hence, loss of diversity or a fraction of diversity.
New Research Proves Single Origin Of Humans In Africa
ScienceDaily (July 19, 2007) — New research published in the journal Nature (19 July) has proved the single origin of humans theory by combining studies of global genetic variations in humans with skull measurements across the world. The research, at the University of Cambridge and funded by the Biotechnology and Biological Sciences Research Council (BBSRC), represents a final blow for supporters of a multiple origins of humans theory.
Competing theories on the origins of anatomically modern humans claim that either humans originated from a single point in Africa and migrated across the world, or different populations independently evolved from homo erectus to home sapiens in different areas.
The Cambridge researchers studied genetic diversity of human populations around the world and measurements of over 6,000 skulls from across the globe in academic collections. Their research knocks down one of the last arguments in favour of multiple origins. The new findings show that a loss in genetic diversity the further a population is from Africa is mirrored by a loss in variation in physical attributes.
Lead researcher, Dr Andrea Manica from the University's Department of Zoology, explained: "The origin of anatomically modern humans has been the focus of much heated debate. Our genetic research shows the further modern humans have migrated from Africa the more genetic diversity has been lost within a population.
"However, some have used skull data to argue that modern humans originated in multiple spots around the world. We have combined our genetic data with new measurements of a large sample of skulls to show definitively that modern humans originated from a single area in Sub-saharan Africa."
The research team found that genetic diversity decreased in populations the further away from Africa they were - a result of 'bottlenecks' or events that temporarily reduced populations during human migration.They then studied an exceptionally large sample of human skulls. Taking a set of measurements across all the skulls the team showed that not only was variation highest amongst the sample from south eastern Africa but that it did decrease at the same rate as the genetic data the further the skull was away from Africa.
To ensure the validity of their single origin evidence the researchers attempted to use their data to find non-African origins for modern humans. Research Dr Francois Balloux explains: "To test the alternative theory for the origin of modern humans we tried to find an additional, non-African origin. We found this just did not work. Our findings show that humans originated in a single area in Sub-Saharan Africa."
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quote:Originally posted by MindoverMatter718: Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa
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.
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quote:Originally posted by MindoverMatter718: 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.
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.
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quote:Originally posted by The Explorer: ^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].
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posted
Watch out! The b*tchass troll that ruined the original thread of this topic might scurry back here to revive his idiotic argument that Euros are not mixed via Bowcock study! LOLPosts: 26252 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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The point seems to be that there is more variation in population within Africa and populations further from Africa have less variation.
However distance doesn't explain why there is variation to begin with within Africa therefore I think the title could have been better worded. Climate is usually associated with a whole population not within-population phenotypic diversity.
Natural selection may confer an adaptive advantage to individuals in a specific environment if an allele provides a competitive advantage. Alleles under selection are likely to occur only in those geographic regions where they confer an advantage. The second main cause of genetic variation is due to the high degree of neutrality of most mutations. Most mutations do not appear to have any selective effect one way or the other on the organism. The main cause is genetic drift, this is the effect of random changes in the gene pool. In humans, founder effect and past small population size (increasing the likelihood of genetic drift) may have had an important influence in neutral differences between populations.
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quote:Originally posted by the lion: However distance doesn't explain why there is variation to begin with within Africa therefore I think the title could have been better worded.
The point here is that after the ancestors of non Africans left Africa, they went through numerous bottlenecks outside of Africa, which decreased their populations diversity phenotypically and genetically the further they went. This is better understood when you learn that all non Africans are nothing more than a subset of Africans who left Africa and traveled around the world, while enduring bottlenecks wherein each time genetically and phenotypically diversity was decreased.
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posted
Have you heard of the recent article that showed Indians to be as diverse as East Africans?
Posts: 1502 | From: Dies Irae | Registered: Oct 2010
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posted
^ No. Which article is this? This is not at all surprising since we all know India was the great cul-de-sac of early Out-of-African migrants. This can be seen in the M cladistic diversity there.
quote:Originally posted by the lyinass: There article's title is confusing.
Of course it is to stupid ignoramuses like you. As Mind has explained Africa was the original source population of all humanity as a subset left Africa to populate Eurasia, they carried less genetic diversity and soon more subsets of this left to populate other parts of Eurasia. Thus the further a population is from Africa, the less diverse they are. Simple as that.
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posted
^I don't even think the dimpled thimble head above even realizes that he has turned right around and kicked himself in the nuts yet again.lol
Posts: 676 | From: the Alpha and the Omega | Registered: Nov 2010
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quote:Originally posted by L': Have you heard of the recent article that showed Indians to be as diverse as East Africans?
That study was flawed.
They only scanned a very minor region of the genome. If more genomic regions were included this would not hold true.
Posts: 695 | From: وكان المصريون القدماء القوقازين | Registered: Jan 2011
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posted
^ Can you cite the actual study so we'll know what you're talking about?
quote:Originally posted by A Simpleton: I don't even think the dimpled thimble head above even realizes that he has turned right around and kicked himself in the nuts yet again.lol
I don't think you'll be able explain why think the above of me, since I've never done such a thing unlike YOU who has shot yourself in the foot and face countless times. I'm waiting.
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