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[QUOTE]Originally posted by Mystery Solver: [QB] [QUOTE]Originally posted by alTakruri: Sure it answered the question, and quite fully, with a direct quote straight from Arredi who issued it. [QUOTE]Originally posted by Mystery Solver: Originally posted by alTakruri: See Arredi 2004 for the moot TRMCA. [QUOTE] The TMRCAs for E3b (8.3KY, 95% CI 5.2–12.4 KY; or 14.4 KY, 95% CI 9.3–19.3 KY; table 2) and E3b2 (2.8–8.2 KY) should thus bracket the spread of E3b2 in North Africa. These times contrast sharply with estimates of 53 ± 21 KYA for the M35 lineage and 32 ± 11 KYA for the M81 lineage, by use of a constant-sized population model, or 30 ± 6 and 19 ± 4 KYA, respectively, by use of an expanding population model (Bosch et al. 2001). They are, however, more in accordance with times of 26.5 KYA (without a useful CI) for the M215 mutation ... and 5.6 KYA for M81 (Cruciani et al. 2004) or of 29.2 ± 4.1 KYA for M35 and 8.6 ± 2.3 KYA for M81 (Semino et al. 2004). [/QUOTE]Doesn’t answer the question at hand, which was: By E3b-M35, are you referring to its derivative E-M81? That date for E3b sounds questionable.[/QUOTE][/QUOTE]In which case, your initial post placing E3b-M35 to just 8ky ago was misleading, because even your citation of Arredi et al. gives [i]both[/i] lower bound and upper bound expansion estimations along with their corresponding CIs, and when the CIs are taken into consideration, the upper bound expansion age falls in the general reach of the Upper Paleolithic as is the case with the dates provided by Semino et al., Luis et al, Cruciani et al. and Underhill et al, with a give-or-take so many years of the dates provided by the said researchers - all dating back to the upper Paleolithic, as opposed to the impression given by your initial post of a Neolithic timeframe. Example 1: [i]The TMRCAs for E3b (8.3 KY, 95% CI 5.2 to 12.4 KY; or 14.4 KY, 95% CI 9.3 to 19.3 KY; table 2) and E3b2 (2.8 to 8.2 KY) should thus bracket the spread of E3b2 in North Africa. These times contrast sharply with estimates of 53 ± 21 KYA for the M35 lineage and 32 ± 11 KYA for the M81 lineage, by use of a constant-sized population model, or 30 ± 6 and 19 ± 4 KYA, respectively, by use of an expanding population model (Bosch et al. 2001). They are, however, [b]more in accordance with times of 26.5 KYA (without a useful CI) for the M215 mutation (intermediate between M35 and M96 in the phylogeny; see fig. 1A) and 5.6 KYA for M81 (Cruciani et al. 2004) or of 29.2 ± 4.1 KYA for M35 and 8.6 ± 2.3 KYA for M81 (Semino et al. 2004).[/b][/i] - Arredi et al. 2004 Example2: [i]We obtained an estimate of 25.6 thousand years (ky) (95% CI 24.3 to 27.4 ky) for the TMRCA of the 509 haplogroup E3b chromosomes, [b]which is close to the 30 ± 6 ky estimate for the age of the M35 mutation reported by Bosch et al.[/b] (2001) using [b]a different method[/b]. Several observations point to eastern Africa as the homeland for haplogroup E3b - that is, it had (1) the highest number of different E3b clades (table 1), (2) a high frequency of this haplogroup and a high microsatellite diversity, and, finally, (3) the exclusive presence of the undifferentiated E3b* paragroup. [/i] - Cruciani et al. 2004 Example 3: [i]A more recent dispersal out of Africa, represented by the E3b-M35 chromosomes, expanded northward [b]during the Mesolithic[/b] (Underhill et al. 2001b). The East African origin of this lineage is supported by the much larger variance of the E3b-M35 males in Egypt versus Oman (0.5 versus 0.14; table 3). Consistent with the NRY data is the mtDNA expansion estimate of 10 to 20 ky ago for the East African M1 clade. Local expansions of this clade and subsequent demic movements may have resulted in the irregular presence of the M1 haplogroup in the Mediterranean area (Quintana-Murci et al. 1999).[/i] - Luis et al. 2004 ^ Naturally the expansion ages of 10 to 20 ky provided by Luis et al. herein, correspond with E-M78 lineages, since ancestral E3b lineages have rarely been found in Northeast Africa [Egypt in this case] as opposed to sub-Saharan East Africa. Example 4: [i]The M35 estimate is [b]in agreement with those of Bosch et al. (2001) and Cruciani et al.[/b] (2004 [in this issue]), obtained with [b]different methods[/b].[/i] - Semino et al. 2004 Semino et al., Underhill et al, and Cruciani et al. have relatively more closer TMRCA ages for E3b [and in turn relatively closer to Bosch et al.’s date for E3b-M35, but produced relatively closer TMRCA ages for E-M81 to Arredi et al. than Bosch et al.] than Arredi et al., but it is also of note that, while these researchers had study sub-Saharan groups in their dating estimations, Arredi et al. in their 2004 publication directly studied only the more Northern African groups; Bosch et al. 2001 started [i]largely[/i] coastal North Africans : [i]To provide a more complete description of the North African pattern of Y-chromosomal variation, we have analyzed five additional populations: Algerian Arabs, Algerian Berbers, Tunisians, and North and South Egyptians (table 1)… In addition, samples from southern Europe, the Middle East, and sub-Saharan Africa were included in some analyses (Semino et al. 2000; Underhill et al. 2000; Cruciani et al. 2002).[/i] - Arredi et al. 2004 Given that these aforementioned researchers did relatively more detailed population genetics analysis on E3b macro-haplogroup than Arredi et al. 2004 [and Bosch et al. 2001], they have an edge over the latter. Arredi et al.’s age estimation for E3b would be a reflection of their analysis of Northeast and Northwest African derivatives of E3b, notwithstanding adopting methodology from other researchers like Zhivotovsky et al. 2004 in the ‘effective mutation rate’. [QUOTE]Originally posted by alTakruri: Actually the highest CI figure in Arredi only goes back 19,300 years. Arredi is really loose with the TMRCAs [QUOTE] E3b (8.3KY, 95% CI 5.2–12.4 KY; or 14.4 KY, 95% CI 9.3–19.3 KY; table 2) E3b M35 226 8.26 (5.18–12.37) 14.33 (9.32–19.19) [/QUOTE]Taking both generation sets into consideration it's anywhere from 5,200 years ago to 19,300 years ago but the 23,000 year figure is out of Arredi's range. Table 2 TMRCA Estimates and 95% CIs of Y-Chromosomal Lineages in North Africa [/QUOTE]The 23 ky ago so was estimation based on Cruciani et al. [actually reflecting upper bound expansion of E3b1], who had actually done more extensive sampling on and 'combing' of E3b chromosomes than Arredi et al. Arredi et al. base their calculations on the dating methods by following researchers: [i]The TMRCA of haplogroup E3b2 was estimated to be ~ 4.2 KY (95% CI 2.8 to 6.0 KY), using the mutation rate measured in father-son pairs (Kayser et al. 2000) and assuming 30 years per generation, or 6.9 (5.9 to 8.2) KY using the deduced "effective" mutation rate calibrated by historical events (Zhivotovsky et al. 2004) (table 2). a The two parameters describing the population growth (alpha and beta) have been set as alpha prior uniform (0.03, 0.05) and beta prior uniform (0.10, 0.20), the microsatellite mutation rates used were from Weale et al. (2001) or gamma (2,1000) for the loci for which published estimates of mutation rates were not available. b The two parameters describing the population growth (alpha and beta) have been set as in footnote a, the microsatellite mutation rate used was from Zhivotovsky et al. (2004).[/i] - Arredi et al. 2004 …and were apparently not the only researchers to adopt the methodology utilized by Zhivotovsky et al., since Cruciani et al. 2007 too employed the following methodology: And again from Cruciani et al., we have: [i]To estimate the time TMRCA of haplogroups we used the seven tetra nucleotide loci and applied the average square distance (ASD) method (Goldstein et al. 1995), where the ancestral Haplotype was assumed to be the Haplotype carrying the most frequent allele at each micro satellite locus. [b]We employed a micro satellite evolutionarily effective mutation rate (Zhivotovsky et al. 2004). However, since the loci used here and those used by Zhivotovsky et al. (2004) do not overlap completely, we calculated the micro satellite mutation rate as follows[/b]: we obtained the mean and standard deviation of the father-to-son mutation rates reported by Gusmao et al. (2005) for the same loci here used, and reduced them by a factor 3.6 [i.e. the discrepancy between the rate estimate obtained from population data and that obtained from father-to-son transmissions (Zhivotovsky et al. 2004)]. This resulted in an evolutionarily effective rate w=7.9 x 10^-4 (SD=5.7x10^-4), a figure that was also used in recalculating the E-M215 coalescence age (data from Cruciani et al. 2004). Recently, Zhivotovsky, Underhill and Feldman (2006), showed that reduced loss of diversity in an expanding population brings the [b]evolutionarily effective rate closer to the germ-line rate than in constant-size populations[/b]. Thus, in the case of expanding populations, we used a correction of the 7.9 x 10^-4 value, that was calculated as follows. With reference to fig. 2 in [b]Zhivotovsky, Underhill and Feldman [/b] (2006), the values of accumulated variance in 200-300 generations for the scenarios of 1)a single rate for exponential population growth and 2) growth with four distinct consecutive rates, were compared with the amount accumulated in constant size populations. This resulted in evolutionarily effective mutation rates decreased of factors 2.4 and 2.8 respectively (instead of 3.6), that is 11.9 x 10^-4 (SD = 8.5 x 10^-4 and 10.2 x 10^-4 (SD = 7.3 x 10^-4), which were applied to Haplogroups E-V13 and J-M12 found in Europe. C.I.s for the ASD (and TMRCA) were obtained as follows: mutations on the micro satellite genealogy were simulated using a Poisson process, in which the total number of mutational events was calculated based on branch length and assuming that mutations at each micro satellite were gamma-distributed with mean and standard deviation calculated as above. Each mutation increased or decreased allele length by one step (each with probability 0.5). ASD was then evaluated for the simulated data and the whole process repeated 1000 times, to quote the central 95% values. This method represents a refinement of that by Thomas et al. (1998) and Scozzari et al. (2001), as it also takes into account [b]heterogeneity of mutation rates across loci.[/b] And independent dating method (rho statistics; Forster et al. 1996 et al. 1996; Saillard et al. 2000) was also used to assay how robust the time obtained is to choice of method. Both dating procedures [b]rely on the appropriate choice of a Haplotype to be considered ancestral, which remains an uncontrolled source of uncertainty. [/b] We observe that the rho-based ages are slightly younger than the ASD-based ones (fig. 1). The difference is significant only for the root of the entire Haplogroup, this being attributable to the relevant departure from a star-like structure because of repeated founder effects (Saillard et al. 2000). Only values obtained from ASD are quoted in the text. Haplogroup diversity and its sampling variance were estimated as in Arlequin 3 (Excoffier, LAVal and Schneider 2005).[/i] - Cruciani et al. 2007 [QUOTE]Originally posted by al Takruri: If we can back up from this tree and look at the forrest, the point I'm making is that there's no general agreement on these TMRCAs between Bosch, Arredi, Cruciani, and Semino. Most certainly not so for a 23,000 year ago date for E3b. [QUOTE] Originally posted by Mystery Solver: Notice that these datings are given with confidence intervals which shouldn’t be dismissed. Once taken into account, the age provided for E3b doesn’t deviate much from the general understanding that E3b originated in the Upper Paleolithic, in the vicinity of ca. 23 ky ago [b]or so[/b].[/QUOTE][/QUOTE]Subtlety of language can make quite a difference: For instance, in my posted cited, there’s [i]“in the vicinity of"[/i] and [i]“or so”[/i]; therefore, the claim about the findings of all the said researchers’ fitting the 23 ky ago date specifically, is but a smokescreen. Furthermore, in my post, it was mentioned [i]“E3b originated in the upper Paleolithic”[/i], which undoubtedly contradicts the date you focused on in your post - that is, the 8 ky ago figure. As you have read in the words right from the very authors that you cited, there is a [i]“general”[/i] agreement between them with respect to the other researchers they‘ve cited. See the topmost postings of this entire post, in the ‘examples’ provided for this. [/QB][/QUOTE]
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