User:Pdeitiker/Temp

Time of Y-Adam
The first efforts to determine the most recent common ancestor of Y-Adam were based on the ZFY-locus. The  study found no differences between any of the 38 men studied, indicating a small but indefinite population size that could have arisen anywhere. The mutation rate used was anchored in Chimp, gorilla, orangutan, and baboon phylogeny. Two different modes based on different assumptions were proposed. The first, 270,000 BP, was based on a coalescent model and flat population structure. The second model assumed a growth structure which allows a much more rapid (radiative) expansion with a mode at 27,000 BP. With no observed variation the range relative to the mode is great and there were a large number of interpretations, with TMRCAs ranging from 0 to 3,430,000 years. All studies relied heavily on population size assumptions (frequently taken from mtDNA MRCA studies), CHLCA dates, growth, and selection; however, the majority of critiques noted few insights on TMRCA or long-term effective size of men.

examine 100,000 base-pairs of DNA from the non-recombining region of the Y chromosome in 6 males, 5 humans and 1 chimapanzee. The found a likely TMRCA between 37,000 and 49,000 BP. This TMRCA held for a long period because it agreed with recent expansion scenarios from Africa. This range was widely touted in the literature for almost a decade. undertook the effort to look at biallelic (Single nucleotide polymorphisms, SNP) mutations. Some of these markers, like M17 are still used to identify haplogroups like R1a1a. This study assumed a population size of males of 5000 individuals and using two data sets estimates TMRCAs of 162,000 BP or 186,000 BP, both with wide confidence ranges. One of the major problems with using biallelic markers is there is a requirement of sample density between the deepest branches, even though the human genome project has produced one complete Y-sequence, the sequence for the deepest branch, no determined to be Haplogroup A/BT needs to be determined, then adequate regions of Haplogroup A need to be sequenced (as the human genome projects sequenced haplgroup BT representative). Getting a full representation of the biallelic markers has proven difficult.

Another technique to measure branch distances involves the STR, however molecular clocking of STR has proved controversial. have used STR and 51 haplogroup defining SNPs to re-examine the a characterized collection (called HGDP-CEPH) and determine a TMRCA about 120,000 BP with a range that was above the Whitfield estimate and below the Underhill et al. 1997 estimate.

Population Structure
Population structure is a major determinant of the TMRCA. However the demonstration of a population structure about the time of Y-chromosomal Adam has been difficult to determine.(See Early modern human population structure) One problem of the early studies was the lack of variation of intricate phylogenetic tree, many different assumed structures could produce the observed tree. For example, the star phylogeny used by Dorit could have arisen from a single male ~25,000 years ago or by Bayesian estimate of 20,000 males almost a million years ago. In, fact without variation it is only possible to set an upper limit of population sizes. The intricacies of SNP variation in the Y-chromosomal family tree has been difficult to establish. Many authors have relied on STR variation, however many studies do not account for complex rate variation between STR sites. And STR variation of the fastest evolving sites is not useful for clocking in the deepest level of the Y-DNA family tree. Other problems also exist; the small numbers of biallelic markers and the difference between chimpanzee and human Y-chromosomal evolution rate (the Testis effect) and made it difficult to detail structure over time or correctly anchor the chimp-human MRCA sequence. Until recently estimates of 500 to 1500 effective males reflect commonly stated TMRCA of 25,000 to 75,000 years. More recently however the estimates of population size have been increasing.

A most recent study based on STR and SNP polymorphisms placed effective male population size at 2100. This population size can be critiqued on several grounds. The first two critiques are based in the TMRCA estimate of 117,000 BP itself (However this estimate has to be tempered against the several in going critiques. First, "evolutionary" clocking based on STRs is extremely controversial, particularly for very recent (genealogy) and ancient time estimates (much older than 60,000 years). Second, only 51 SNP variants were typed, this compares with >10,000 mutational events detected in Soares et al. 2009 (for mtDNA). Observation from mtDNA that within the last approximately 80,000 years their appears to have been a substantive asymmetric expansion of the human population, this can also be noted in the current SNP defined haplogroup family tree, with the CF and D branches of the tree primarily branching out of Africa. However because of the greater uncertainty of the TMRCA with Y-chromosome relative to mtDNA the differential time (i.e. the constrict time) is currently difficult to assess, but suggests a much smaller size.

An assumption based method used in the literature would be to base male population size on female population size assuming a 1 to 1 female to male ratio. With current female population size estimated, this would place size between 1,100 and 11,000 effective males based on a genetic genetic model. However 2 recent studies indicate that the more appropriate male to female ratio would 1:2 and would assume population sizes of 550 to 5500 males with a maximum likelihood around 1700 males. Within this assumption the 2100 effective male estimate with or without early inflection is tolerable (assumed by mtDNA and Hg branching; assume Y-DNA TMRCA exceed 100,000 BP and mtDNA MRCA fall below 200,000 BP). However lower TMRCA for Y-DNA might violate a genetic drift assumption and suggest a selective component to an early expansion. In either case it would appear that the wide range of population sizes originally postulated by Dorit et al. 1995 have slowly been chiseled into a range that is parsimonious with the expansion of mtDNA from Africa. As discussed below this coincides with a potential origin of Y-chromosome from a wide number of Old World possibilities to a probable origin in sub-Saharan Africa.

Place of Y-Adam
Hammer 1994 examined a set of Alu polymorphism and determined a slightly increased diversity in Africa. Dorit et al. 1995 found no variation at the ZFY locus and therefore the placement of the MRCA was uncertain. A later recent study found another element with greatest diversity in the Chinese. Single binary markers have proven to be speculative in determining the place of the MRCA. Large collections biallelic SNP markers on the Y chromosome have proven to be more useful, Underhill et al 1997 did the first widescale survey of markers. Since then many more markers have been uncovered that have allowed the more probable placement of his M2, M8 markers into the Macrohaplogroups A, BT, B, CT, CE and CF. This phylogenetic tree clearly favors a common origin in Africa. The recent study by Shi et al. 2009 places the origin of Y chromosome within the San (!kung) an arid climate hunter- gatherer society in Southwestern Africa (Namibia, Botswana, South Africa). This placement is based on the frequency of A and B haplogroups (The two deepest branching haplogroups) in Southern Africa. This placement differs with that of MRCA of human mtDNA within the Tanzania region. However the placement of the Y-MRCA later and within the region is consistent with a major split observed by Behar et al. 2008 that occurred approximately 140,000 BP, and uncertainty in the temporal placement of the mtDNA L0k branch and Y-MRCA are widely tolerant of overlap.

However both Behar et al. 2008 and Shi et al. 2009 suffer from an acute lack of sampling in certain regions of Africa (e.g. Angola, S. Congo), regions close to or juxtaposed on putative points of fission or origin. In addition, for Y-MRCA there has been a recent spread of haplogroup E from the north, either as part of the Bantu expansion, or as part of earlier expansions associated with haplogroup L3 from East Africa. The greater influence of Y-chromosome may have caused a partial displacement of haplogroups A and B over certain regions of Southern Africa, biasing the interpretation of the place of the MRCA.