All this demonstrates that, despite variation in estimates of average Y-STR effective mutation rate (variations due to uncertainties in archaeological/historical data and in male/female population dynamics), these estimates are close to the overall point estimate ( per 25 years) and lie within the interval defined by SE, which is attributable to differences between loci. Doubling the SE, we obtain and as heuristic confidence limits for w. Potential errors in estimates of w
attributable to uncertainties in archaeological/historical records (see the first two paragraphs of the present section) lie within these limits. Therefore, variation among loci in effective mutation rate of various loci may be a major source of deviation of an average estimate of w from a true value for Y chromosome STRs.
Between-Locus Variation in the Effective Mutation Rate
Mutation rates are reported to vary substantially among autosomal microsatellites (Di Rienzo et al.1998; Zhivotovsky et al. 2001); the same is expected for Y chromosome STRs (Forster et al. 1998; Kayser et al.2000b;
Nebel et al. 2001). On the basis of our data, we calculate that the coefficient of between-locus variation in effective mutation rate is 0.00057/0.00069 ; a similar level of between-locus variation in effective mutation rate has been observed for autosomal loci (Zhivotovsky et al. 2001). Although sampling errors contribute to this variation, the differences in w between loci are nevertheless important. Indeed, mutation rates can vary from locus to locus, depending on their structure. Forexample, DYS389 is a complex locus consisting of four tetranucleotide-repeat subloci (Cooper et al.1996; Rolf et al. 1998) that yield two distinctive fragments when genotyped using conventional protocols,since the forward primer anneals twice. One fragment contains all four repeat motifs (A, B, C, and D), and the other fragment, which contains just two (C and D), is often denoted by “I”. The shorter CD fragment is subtracted from the larger to yield the AB (“II”) allele. Itis important to note that the C motif is almost alwaysonly three repeats and thus is monomorphic, whereas the longer combined AB motifs are both polymorphic,thus making the AB region more mutable than the CD region. The sublocus DYS389AB can be treated as aseparate microsatellite locus that has an inherentlyhigher mutation rate than the CD sublocus. This genomic complexity and the consequent differential mutation properties of the subloci are expected to increase the overall mutation rate for DYS389. Removing DYS389 from the analysis gives . Counting that locus twice produces the same value, 0.00061. However, it is difficult to conclude that DYS389AB or other such loci will always behave—in UEP lineages or entire populations—as loci with high mutation rates,and more data will be needed to distinguish loci with different effective mutation rates. Another source of apparent between-locus variation may be different mutation rates for alleles with different numbers of repeats(Brinkmann et al. 1998). This variation actually occurswithin a locus and can greatly confound between- andwithin-locus variation. Probably, our estimate of SD,, includes both kinds of variability and therefore encompasses an entire range of “between-allele”variation.Variation in mutation rates should be kept in mind,because it might be a major source of uncertainty whena small number of loci are used. The large SE of the average mutation rate obtained here and the large SE of divergence time estimates (see below) reflect such variation. (Note that highly variable Y chromosome haplotypes cause very big CIs for coalescent times based on microsatellites [Pritchard et al. 1999]).Therefore,datinghistorical events on the basis of a small number of Y-STR loci might disagree with historical/archaeologicalrecords, although the latter might also have large “SEs.”Theoretically, hundreds of loci may be needed for precise dating of ancient demographic events (Zhivotovsky andFeldman 1995; Goldstein et al. 1996; Jorde et al. 1997), and different subsets of loci may give different estimates because of different mutation rates (Zhivotovsky et al.2003). Analysis of population divergence within UEP lineages should require fewer microsatellite loci for precise dating, because STR variation within a UEP lineage must be smaller than that in the entire UEP-heterogeneous population. The sample of Y chromosome STR loci (no more than 10 were used here) still seems too small, and a larger number of loci need to be analyzed (e.g., Seielstad et al. 2003), and
150 new Y-STRs will be available in the near future (M.Kayser, M.A.Jobling, A. Sajantila, C. Tyler-Smith, unpublished data). Fu–thermore, we cannot exclude the possibility that mu-tation rates at the same STR locus vary among haplo-groups because of differences in allele repeat scores, repetitive structures, or other factors (Nebeletal.2001); mutation rates might also be population specific, because of variation in genes that encode proteins involved in DNA replication and repair mechanisms or proteins that cause associated selection, if these exist (see Jobling and Tyler-Smith 2000). A large sample of loci might decrease these possible effects, but, in the absence of hard information, it seems reasonable to use the same overall average mutation rate for all instances.The estimates of average effective mutation rate and the SD can be used to obtain a two-parameter prior distribution for Y chromosome effective mutation rates for use in coalescent models.
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The origin and time of arrival of the Samoans are inquestion. The tree in figure 3 shows that the Samoans split much earlier than the ancestral population that gave rise to the Maoris and Cook Islanders. Recall that theMaoris arrived in New Zealand 800–1,000 years BP; together with the time estimate between the two separation events in figure 3, this implies ∼ 3,500 years BP for divergence of the Samoans from a common ancestral population. This can be compared with the time of East Polynesian settlement, estimated to have occurred by 500–1000 BC (Irwin 1992, p. 81), and to the estimate of the early peopling of Polynesia, 3,000–4,000 years BP (Underhill et al. 2001a ).
Divergence between the Gypsy Populations
Computation of TD values averaged over all possible pairs of the 10 Gypsy populations (omitting both the Darakchii, with one M82 individual only, and the Musicians) and gives us an estimate of the time of founding of an ancestral population of related males sharing the same Y haplotype that gave rise to the contemporary Bulgarian Gypsy populations. This estimate gives 1,500-700 BC an upper bound for the divergence time and is compatible with the formation of the proto-Gypsies in India,predating their entry into the Byzantine Empire 900–1,000 years BP (Fraser 1992). If diversity was already substantial in the founder male population, and the estimate of divergence time would be smaller. The genetic composition of the Musicians differs greatly from that of the other studied Bulgarian Gypsy populations, a fact that points to possible differences in their evolutionary history. There are two possible explanations for this: the Musicians share the same origin but were greatly admixed with populations from South Asia that carried the M82 mutation, or they descended from an ancestral population different from that of the other Bulgarian Gypsy populations studied. The origins of the proto-Gypsies, as well as the time and number of migrations out of India, are still disputed among cultural anthropologists and linguists (Fraser 1992; Marushia-kova and Popov 1997; Hancock 2000). Our previous study (Gresham et al. 2001) suggested a common origin from a small group of ancestors. One should note, however, that the Musicians were not included in that study and that they are the sole representatives of a particular Balkan dialect of the Romanes language. In addition to the unusual distribution of M82 haplotypes, they display a generally higher diversity of Y chromosome lineages, including other uncommon types, that are unlikely to result from European admixture. If we follow the “different origins” scenario, the TD estimator gives an upper bound of 2,600 years BP for the separation of the Musicians from a population ancestral to the other studied populations of Bulgarian Gypsies. The difference of 1,100 years between the two splits (fig. 4) allows not only for heterogeneous origins but also for the possibility of different proto-Gypsy migrations from the Indian subcontinent.
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