User talk:Wobble/Race genetics and human evolution

Multiregional hypothesis
This hypothesis assumes that Homo sapiens evolved independently in many different regions from Homo erectus about two million years ago. Scientists generally agree that this would result in a great deal of diversity in the global modern Homo sapiens population. Recent evidence from molecular biology indicates that Homo sapiens is too genetically homogeneous to have evolved independently several times. Much evidence indicates a genetic bottleneck at some time in our recent past, indicationg that our origins are probably not diverse. "Gene flow among these populations, combined with natural selection for advantageous genes, maintained genetic homogeneity of the species. Under this hypothesis, our species had hundreds of thousands, perhaps millions, of ancestors for most of the last million years. Without a large population, gene flow among populations distributed widely over the temperate and tropical Old World would have been impossible.....If the size of the human population had been large throughout much of its history, extant genetic variation should be substantial. Conversely, a small human population would result in relatively little genetic variation." So this hypothesis calls for a large and globally freely interbreeding population, that is no geographical separation between populations that are spread over a wide area. This hypythesis would mean a very large deree of genetic diversity globally, this is not supported by genetic evidence. In my opinion much of this hypothesis seems to be derived from 18th and early 19th century attempts to classify all archaic hominids as ancestral to modern humans in an attempt to show progression from primitive to advanced. A more correct understanding is that evolution is not progressive but adaptive, all species are well adapted to their environment, extinctions do not arise due to primitive traits being replaced by advanced traits, but to environmental stress. So a more correct interpretation of events is that archaic hominids were not made obsolete by more advanced modern humans. I think multiregionalism does not make much sense from an evolutionary point of view, how can the same species arise in several different geographical places independently at the same time?

Assimilation model
Confusingly this theory is often also sometimes called the "Multiregional Hypothesis". This is effectively a modified multiregional model, as it became increasingly difficut to accept the multiregional hypothesis, multiregionalists modified their model to include an Out of Africa element. This is the theory that modern humans evolved in Africa recently, but that a lot of genetic exchange occured between local archaic hominids and AMH people as they populated different regions of the world. This theory seems to be mainly based on the discovery of neanderthal like AMH and AMH like neanderthal remains. This may indicate that there was some reproduction between the two populations is Europe. Of course it doesn't tell us whether these hybrids transmitted their genetic legacy to modern humans, the fact they existed is not the same as showing their progeny survived, or that they contributed biologically to modern humans. The other problem with this hypothesis is that AMH and neanderthals were very biologicaly different, much more different than modern populations are from each other. So this leads to the problem of outbreeding depression, this phenomenon only applies to unrelated or distantly related populations such as Homo sapiens sapiens and Homo sapiens neanderthalis/Homo neanderthalis. "However, even if we accept controversial claims for the existence of supposed Neanderthal–modern hybrids (e.g. Duarte et al. 1999), it is well known that many closely related mammal species (including primates) can hybridize, and may even produce fertile offspring. However, if this is not a widespread or reproductively successful behaviour, it may have little or no impact on the populations that constitute the core of the different species or on future generations. The limited genetic data on Neanderthal–recent relationships show that Neanderthals and recent H. sapiens represent distinct but nevertheless closely related lineages, but are ambiguous about whether these samples represent different species. Thus, in fossils, morphological criteria necessarily remain the mode of species recognition, but recent research is providing better testing of the assumptions involved.... Harvati (2001) used differences in temporal bone morphology between common chimpanzees and speciﬁcally distinct bonobos to compare the level of difference between Neanderthals and recent H. sapiens. She concluded that Neanderthal–recent differences in the temporal bone were at least as great as those between the two chimpanzee species. As she recognized, this result was based on only one cranial area, and further tests were required before reaching more deﬁnitive conclusions. In a similar study based on cranial measurements, Schillaci & Froehlich (2001) compared the level of differentiation of fossil (Upper Palaeolithic) H. sapiens and Neanderthals with that calculated between species of macaques that are known to hybridize, or not to hybridize. Again, the degree of difference between the fossil human cranial samples exceeded that found between the recent primate species. Thus, both these studies supported the distinctiveness of H. neanderthalensis." Some researchers are now claiming that the human genome is different from mtDNA and represents a "mosaic" that may be derived from ancient and modern hominids. This theory would mean that hominids are a relatively promiscuous freely interbreeding group of organisms and that all hominids, from H. erectus to Neanderthals to AMH freely shared their genetic material.

Out of Africa 2
This seems to be the most generally accepted model for human origins. It infers that AMHs expanded out of Africa from a small human bottleneck population (about 10,000). The expansion is thought to have occured about 100,000 years ago, with anatomically modern humans (AMH) having evolved about 190,000 years ago. All human populations outside of Africa would represent a sub-set of African populations, with most diversity being observed in sub-Saharan Africa. A small contribution to modern humans from archaic humans is not discounted but may be unlikely.

Human genetic variation
Human genetic variation is small compared to other animal populations, supporting a single origin hypothesis. "That is, research reveals that Homo sapiens is one continuously variable, inter-breeding species. Ongoing investigation of human genetic variation has even led biologists and physical anthropologists to rethink traditional notions of human racial groups. The amount of genetic variation between these traditional classifications actually falls below the level that taxonomists use to designate subspecies, the taxonomic category for other species that corresponds to the designation of race in  Homo sapiens. This finding has caused some biologists to call the validity of race as a biological construct into serious question.""The average proportion of neucleotide differences between a randomly chosen pair of humans (i.e. average nucleotide diversity, or π) is consistently estimated to lie between 1 in 1,000 and 1 in 1,500 (refs.9, 10). This proportion is low compared with those of many other species, from fruit flies to chimpanzees11,12, reflecting the recent origin of our species from a small founding population13.....Of the 0.1% of DNA that varies among individuals, what proportion varies among main populations? Consider an apportionment of Old World populations into three continents (Africa, Asia and Europe), a grouping that corresponds to a common view of three of the 'major races'16, 17. Approximately 85-90% of genetic variation is found within these continental groups, and only an additional 10-15% of variation is found between them18-20 (Table 1). In other words, ~90% of total genetic variation would be found in a collection of individuals from a single continent, and only ~10% more variation would be found if the collection consisted of Europeans, Asians and Africans."

Race
Some studies state that because human genetic diversity is geographically distributed it can be used to infer race. These studies use self-defined "race" or infered "population of origin" as a pre-determinant for classification. Other studies show that such a population based approach to sampling introduces an artificial discontinuity into the samples that infers clustering by "population", when in fact the distributions are shown to be clinal when geography based sampling is used. "The absence of strong continental clustering in the human gene pool is of practical importance. It has recently been claimed that 'the greatest genetic structure that exists in the human population occurs at the racial level' . Our results show that this is not the case, and we see no reason to assume that 'races' represent any units of relevance for understanding human genetic history. In clinical practice, the 'classification' of people into 'races,' as recently suggested could perhaps have some justification as a proxy for differences in environmental and other factors of relevance for public health or to help identify rare disease alleles. However, in the absence of other knowledge, most alleles influencing susceptibility to disease or outcome of medical interventions cannot be expected to show significantly different frequencies between 'races.'"

Conclusion

 * 1) There is no consensus about human origins. Science works by observing phenomena and developing theories to explain those phenomena. Experimentation can never prove any theory, but it can disprove a theory. Currently it seems the weight of evidence is with the Out of Africa 2 model, this may not remain the case and there is some genetic evidence for the assimilationist model. The more evidence that comes to light to support any given model, the less likely another model is of representing the truth. The original multiregional hypothesis seems to be dead, it's derivative model, the assimilationist model may be better, though it involves the admixture of two apparently very different hominid groups, something you have stated on numerous occasions is a bad thing. I refer you to your repeated mention of outbreeding depression and derogatory comments about my assimilationism. It seems that by supporting this hypothesis it is you that are the assimilationist. On the other hand the assimilationist model may imply that "archaic" and AMH were actually much closer biologically than has been previously thought, freely exchanging genetic material. Whatever our origins neither model really provides evidence for a deep and ancient "difference" between "races". On the one hand we have a recent origin hypothesis that supports the idea that all humans are closely related because we are of recent origin. On the other we have an assimilation model that supports the idea that all humans are genetically similar because hominids are naturally promiscuous and freely procreate with each other. Neither model is an endorsement of "seperatism" either from the point of view of origins nor from the point of view of behaviour.
 * 2) The concept of "race" is as contentious as ever, there is no real evidence of races from a genetic point of view, simply continuously distributed genetic variation. Some scientists see a structure to this variation that they attempt to categorise as "race", the boundaries to these "races" are arbitrary, and often populations do not fit deffinitively into one or another pre-determined "race", but rather display characteristics of two or more "races". Most of your statements do not seem to represent the academic mainstream as you claim. I can only assume that this claim is due to a determination to ignore evidence that does not fit with your distorted view of the world. Your beliefs are based on faith more than science, you want there to be races, you want humans to have evolved seperately, you want this to be true. Sorry but it's not. We are all the same and you can never change that. We can never go back to the sort of ignorance that we had in the past, however much you might like to. Your biggoted ideas about "race" and "diversity" (which you seem to use as a proxy for "racial purity") and your tacit support for segregationism shows you for what you really are. There are many more scientific papers that I could have used, but it would have taken much longer to cite them all. Alun 09:32, 14 November 2006 (UTC)

Quotes

 * Despite this complexity, genetics researchers have a unique opportunity to reduce at least some of the confusion and controversy surrounding the issues of race, ethnicity, ancestry, and health. They can demonstrate the irrelevance of racial and ethnic labels for pursuing many research questions and health improvement objectives—for example, by clarifying the many ways in which environmental factors that extend across groups interact with biological processes to produce common diseases. By emphasizing the close genetic affinities between members of different groups, researchers can reduce the widespread misconception that substantial genetic differences separate groups. As the complex origins of human traits, behaviors, and diseases slowly are unraveled, how genetics research is conducted could influence whether racial and ethnic discrimination increases or decreases over time......Existing data on human genetic variation support and extend conclusions based on the fossil evidence. African populations exhibit greater genetic diversity than do populations in the rest of the world, implying that humans appeared first in Africa and later colonized Eurasia and the Americas (Tishkoff and Williams 2002; Yu et al. 2002; Tishkoff and Verrelli 2003). The genetic variation seen outside Africa is generally a subset of the variation within Africa, a pattern that would be produced if the migrants from Africa were limited in number and carried just part of African genetic variability with them (Cavalli-Sforza and Feldman 2003). Patterns of genetic variation suggest an earlier population expansion in Africa followed by a subsequent expansion in non-African populations, and the dates calculated for the expansions generally coincide with the archaeological record (Jorde et al. 1998). Aspects of the relationship between anatomically modern and archaic humans remain contentious. Studies of mtDNA (Ingman et al. 2000), the Y chromosome (Underhill et al. 2000), portions of the X chromosome (Kaessmann et al. 1999), and many (though not all) autosomal regions (Harpending and Rogers 2000) support the “Out of Africa” account of human history, in which anatomically modern humans appeared first in eastern Africa and then migrated throughout Africa and into the rest of the world, with little or no interbreeding between modern humans and the archaic populations they gradually replaced (Tishkoff et al. 2000; Stringer 2002). The Use of Racial, Ethnic, and Ancestral Categories in Human Genetics Research: Race, Ethnicity, and Genetics Working Group, National Human Genome Research Institute, Bethesda. Am J Hum Genet. October 2005; 77(4): 519–532. Published online August 29, 2005.


 * Since the highest π value is only 0.11 %, which is about one order of magnitude lower than those in Drosophila populations, the nucleotide diversity in humans is very low.: Low Nucleotide Diversity in Man by W. H. Li and L. A. Sadler. Genetics. 1991 October; 129(2): 513–523.


 * They also showed that groups that live on the same continent were typically more similar to each other than groups from different continents. However, in all of these studies, the identities of groups and individuals were assigned a priori. In other words, ancestry information such as race, ethnicity or geographical origin was used in conjunction with genetic data to infer group boundaries and allocate individuals to groups. If individuals were stripped of all prior information about ancestry (such as geographical location of origin, race, ethnic group) and assigned to groups a posteriori using only genetic data, it was less clear that geographical origin or racial categories provided reliable information about population structure.:DECONSTRUCTING THE RELATIONSHIP BETWEEN GENETICS AND RACE by Michael Bamshad, Stephen Wooding, Benjamin A. Salisbury and J. Claiborne Stephens. Nat Rev Genet. 2004 Aug;5(8):598-609.


 * it is essential to point out that 'race' and 'ethnicity' are terms without generally agreed upon definitions. Both carry complex conotations that refelct culture, history, economics and political status, as well as a variably importanr connection to ancestral geographic origins.: What we do and don't know about 'race', 'ethnicity', genetics and health at the dawn of the genome era. by Francis S Collins. Nature Genetics Supplement 2004, 36:11, s13-s15.


 * Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. Genetic variation, classification and 'race by Lynn B Jorde & Stephen P Wooding, Nature Genetics' 36, S28 - S33 (2004).


 * ''A clearer picture of human evolution has emerged from numerous studies over the past decade using a variety of genetic markers and involving indigenous populations from around the world. In summary, populations outside Africa derive from one or more migration events out of Africa within the last 100,000 years. The greatest genetic variation occurs within Africans, with variation outside Africa representing either a subset of African diversity or newly arisen variants. Genetic differentiation between individuals depends on the degree and duration of separation of their ancestors. Geographic isolation and in-breeding (endogamy) due to social and/or cultural forces over extended time periods create and enhance genetic differentiation, while migration and inter-mating reduce it.....The results are the same irrespective of the type of genetic markers employed, be they classical systems, restriction fragment length polymorphisms (RFLPs), microsatellites, or single nucleotide polymorphisms (SNPs).....Effectively, these population genetic studies have recapitulated the classical definition of races based on continental ancestry - namely African, Caucasian (Europe and Middle East), Asian, Pacific Islander (for example, Australian, New Guinean and Melanesian), and Native American.....The terms race, ethnicity and ancestry are often used interchangeably, but some have also drawn distinctions. For the purpose of this article, we define racial groups on the basis of the primary continent of origin......The continental definitions of race and ancestry need some modification, because it is clear that migrations have blurred the strict continental boundaries. For example, individuals currently living in South Africa, although currently Africans, have very different ancestry, race and ethnicity depending on the ancestry of their forbears (for example from Europe or Asia) and the degree to which they have remained endogamous. For our purposes here, on the basis of numerous population genetic surveys, we categorize Africans as those with primary ancestry in sub-Saharan Africa; this group includes African Americans and Afro-Caribbeans. Caucasians include those with ancestry in Europe and West Asia, including the Indian subcontinent and Middle East; North Africans typically also are included in this group as their ancestry derives largely from the Middle East rather than sub-Saharan Africa. 'Asians' are those from eastern Asia including China, Indochina, Japan, the Philippines and Siberia. By contrast, Pacific Islanders are those with indigenous ancestry from Australia, Papua New Guinea, Melanesia and Micronesia, as well as other Pacific Island groups further east. Native Americans are those that have indigenous ancestry in North and South America. Populations that exist at the boundaries of these continental divisions are sometimes the most difficult to categorize simply. For example, east African groups, such as Ethiopians and Somalis, have great genetic resemblance to Caucasians and are clearly intermediate between sub-Saharan Africans and Caucasians. Categorization of humans in biomedical research: genes, race and disease'' Neil Risch, Esteban Burchard, Elad Ziv and Hua Tang. Genome Biology 2002, 3:comment2007.1-2007.12


 * The distribution of human genetic diversity has long been a subject of interest, and it has important implications for human evolution, forensics, and the distribution of genetic diseases in populations. Genetic diversity in human populations is low relative to that in many other species, attesting to the recent origin and small size of the ancestral human population (Li and Sadler 1991; Crouau-Roy et al. 1996; Kaessmann et al. 1999b). The proportion of diversity that exists between human populations is also relatively low. An early study, based on protein polymorphisms, arrived at a between-groups diversity estimate of 15% (Lewontin 1972). Other studies, based on protein polymorphisms as well as on blood groups and craniometrics, have yielded similar results (Nei and Livshits 1990; Relethford and Harpending 1994). Recently, surveys of mitochondrial (Merriwether et al. 1991), Y-chromosome (Hammer et al. 1997), and various types of autosomal polymorphisms (Bowcock et al. 1991; Batzer et al. 1994; Deka et al. 1995a, 1999; Jorde et al. 1995; Watkins et al. 1995; Barbujani et al. 1997; Stoneking et al. 1997) have all shown that most human genetic diversity is found within, rather than between, populations. The Distribution of Human Genetic Diversity: A Comparison of Mitochondrial, Autosomal, and Y-Chromosome Data'' by L. B. Jorde, W. S. Watkins, M. J. Bamshad, M. E. Dixon, C. E. Ricker, M. T. Seielstad, and M. A. Batzer. Am J Hum Genet. March 2000; 66(3): 979–988.


 * The extent to which adaptive evolution has shaped the recent evolutionary history of humans is much debated. While polymorphism at certain genes, such as beta-globin or Duffy, is known to be associated with functional variation of selective importance, the functional importance of most DNA variation or substitution since the human-chimpanzee split is unknown. The Influence of Recombination on Human Genetic Diversity by Chris C. A. Spencer, Panos Deloukas, Sarah Hunt, Jim Mullikin, Simon Myers, Bernard Silverman, Peter Donnelly, David Bentley, Gil McVean: PLoS Genetics Volume 2 | Issue 9 | SEPTEMBER 2006


 * The average proportion of genetic differences between individuals from different human populations only slightly exceeds that between unrelated individuals from a single population (4-9). That is, the within-population component of genetic variation, estimated here as 93 to 95% (Table 1), accounts for most of human genetic diversity. Perhaps as a result of differences in sampling schemes (10), our estimate is higher than previous estimates from studies of comparable geographic coverage (4-6, 9), one of which also used microsatellite markers (6). This overall similarity of human populations is also evident in the geographically widespread nature of most alleles (fig. S1). Of 4199 alleles present more than once in the sample, 46.7% appeared in all major regions represented: Africa, Europe, the Middle East, Central/South Asia, East Asia, Oceania, and America. Only 7.4% of these 4199 alleles were exclusive to one region; region-specific alleles were usually rare, with a median relative frequency of 1.0% in their region of occurrence.Genetic Structure of Human Populations'' Noah A. Rosenberg, Jonathan K. Pritchard, James L. Weber, Howard M. Cann, Kenneth K. Kidd, Lev A. Zhivotovsky, Marcus W. Feldman. Science 20 December 2002: Vol. 298. no. 5602, pp. 2381 - 2385


 * The sequences from the two Neandertals differ from those of 663 modern humans sampled from all areas of the world by 34.9plusminus2.4 substitutions and by an insertion of an adenosine residue shared by the two Neandertals. They are not closer to 472 contemporary mtDNAs in Europe (35.3plusminus2.1, range 29−43), the area where they existed until approximately 30,000 years ago, than to, for example, 151 African (33.9plusminus2.8, range 28−42) or 41 Asian mtDNAs (33.5plusminus2.1, range 29−38). This is reflected in a gene tree, where the two Neandertals group together to the exclusion of all modern humans (Fig. 1a). These results do not exclude that interbreeding between Neandertals and modern humans may have taken place9, but they show that even if it occurred, Neandertals did not end up contributing mtDNA to the contemporary human gene pool. A view of Neandertal genetic diversity Matthias Krings1, 8, Cristian Capelli2, 8, Frank Tschentscher3, 8, Helga Geisert4, Sonja Meyer1, Arndt von Haeseler1, Karl Grossschmidt5, Göran Possnert6, Maja Paunovic7 & Svante Pääbo. Nature Genetics 26, 144 - 146 (2000)


 * Although no Neanderthal mitochondrial DNA (mtDNA) lineage is found to date among several thousands of Europeans and in seven early modern Europeans, interbreeding rates as high as 25% could not be excluded between the two subspecies. In this study, we introduce a realistic model of the range expansion of early modern humans into Europe, and of their competition and potential admixture with local Neanderthals. Under this scenario, which explicitly models the dynamics of Neanderthals' replacement, we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species. Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe Mathias Currat, Laurent Excoffier1. PLoS Biology Volume 2 | Issue 12 | DECEMBER 2004


 * We inferred past admixture processes in the European population from genetic diversity at eight loci, including autosomal, mitochondrial and Y-linked polymorphisms. Admixture coefficients were estimated from multilocus data, assuming that most current populations can be regarded as the result of a hybridization process among four or less potential parental populations. Two main components are apparent in the Europeans' genome, presumably corresponding to the contributions of the first, Paleolithic Europeans, and of the early, Neolithic farmers dispersing from the Near East. In addition, only a small fraction of the European alleles seems to come from North Africa, and a fourth component reflecting gene flow from Northern Asia is largely restricted to the northeast of the continent. Estimating the Impact of Prehistoric Admixture on the Genome of Europeans Isabelle Dupanloup, Giorgio Bertorelle, Lounès Chikhi{dagger} and Guido Barbujani. Mol. Biol. Evol. 21(7):1361-1372. 2004


 * In our opinion, the morphological evidence in Europe and the temporal trends discussed previously are most commensurate with the AM and not a model focused on virtually total replacement. Furthermore, we believe the AM is the best fit for the mostly out of Africa genetic perspective reflected in the work of Haprending and Rogers (2000) and others, Relethford (2001), Templeton (2002), and others; and we see the AM being eminently logical in light of the pertinent archaeological evidence. However, we also recognize that we are making a likelihood statement here. The available data do not reject the other models, and there are certainly uncertainties that are critical. As discussed previously, these uncertainties are found in the morphological, genetic and archaeological interpretations on which the AM is based. While fully admitting this, we continue to consider the AM to be the most logical explanation for modern human origins in Eurasia as we understand the phenomenon at the current time. We are convinced that the population dynamics characterizing this phenomenon were very complex. The assimilation model, modern human origins in Europe, and the extinction of Neandertals Fred H. Smith, Ivor Jankovic, Ivor Karavanic. Quaternary International 137 (2005) 7–19