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Post by Admin on Aug 28, 2013 23:29:10 GMT
N1c is the most common haplogroup (47.2%) among the Sami with I1 (25.9%) as a close second and N1c is also found among the Swedish population (10-12%) and the Finns (63.2%) and Rurik, who founded the Rurik Dynasty in 862, belonged to Y-DNA haplogroup N1c1, based on testing of his modern male line descendants. The Sami people have lived in the Scandinavian Arctic over 10,000 years as hunter-gatherers in a harsh environment and they have left their genetic imprint on modern-day Scandinavians just as the Ainu in northern Japan did, who had reached the Japanese archipelago in the same period when the Sami colonised Scandinavia. Both the Sami and the Ainu originated in Siberia and they share a similar culture that they have developed as hunter-gatherers living in the Arctic tundra (i.e. whaling). The predominant Saami Y-chromosomal haplogroup N3 has a nearly uniform circumarctic distribution in Eurasia (table 3). The closely related N2 lineages are frequent in Siberian and Volga-Uralic populations. Thus, it is likely that haplogroup N variation represents a prehistoric link between the Siberian and eastern European/proto-Finnic populations via their paternal heritage. The improved resolution of the Y-chromosomal phylogenetic tree (Jobling and Tyler-Smith 2003) reveals an ancestral node shared by haplogroups N and O, with the latter restricted largely to eastern Asia. This connection is intriguing, but it is still unclear when and where this common ancestor first appeared. Nevertheless, one does not need to postulate a recent Siberian flow of Y chromosomes into the Saami gene pool to explain their high N3 frequency. First, such a flow from Samoyedic-speaking aboriginal Siberians to the Saami Y-chromosomal pool would predict the presence there of haplogroup N2 and/or haplogroup Q, widely spread in Samoyeds (Karafet et al. 2002). Second, the much higher diversity of N3 in eastern Europe than in Siberia (Villems et al. 1998; Rootsi et al. 2000) suggests that eastern Europe, rather than Siberia, is a possible origin of the earliest expansion of this haplogroup in northern Eurasia. Third, the lack of Y-chromosomal haplogroup C in Saami contrasts with its high frequency among Tungusic-speaking native Siberians (such as the Evenks and the Evens) as well as among Mongolic-speaking Mongols, the Buryats, the Kalmyks, and the Turkic-speaking Kazakhs and Uzbeks (Wells et al. 2001; Karafet et al. 2002; authors' unpublished data). Therefore, without introducing specific additional ad hoc scenarios, these observations make it unlikely that there was recent Y-chromosomal flow from these Siberian populations into the gene pool of the Saami. Y-haplogroup N1c entered Europe from Siberia during the Eneolithic period or later. It first appears in the European ancient DNA record in two samples from a burial site at Bolshoy Oleni Ostrov in the Kola Peninsula, dated to 1523±87 calBCE. These individuals also harbor significant genome-wide Siberian ancestry, and north-eastern European populations harbour a Siberian genetic component (light purple) maximized in the Nganasan. Nganasan - the indigenous Siberian people The qpAdm mixture model below is for BOO002 and BOO004, the two males from the Bolshoy Oleni Ostrov site belonging to N1c, and BOO006, a female and the most Siberian-admixed individual from the same site. Although BOO002 and BOO004 show a lot of Nganasan-related and thus Siberian ancestry (0.469±0.017), they also have a moderate input from a source closely related to Baltic_BA from the East Baltic region (0.124±0.029). The individuals BOO002, BOO004 and BOO006 carry mtDNA haplogroups Z1, C4 and D4, common in modern Siberia. BOO002_&_BOO004 Baltic_BA 0.124±0.029 EHG 0.406±0.032 Nganasan 0.469±0.017chisq 10.847 tail prob 0.286316 www.ncbi.nlm.nih.gov/pmc/articles/PMC1181943/
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Post by Admin on Jan 25, 2015 15:45:15 GMT
The Sami are indigenous people inhabiting the Northern Shield, an area including the northernmost parts of Finland, Norway, Sweden and the Kola Peninsula of Russia. The traditional Sami lifestyle is nomadic, based on reindeer herding, fishing and hunting. Sami are the last European population leading a subsistence lifestyle and their traditional diet consists of high amounts of animal products, particularly from reindeer.1, 2 With increased contact with surrounding populations, the lifestyle of the Sami has become increasingly 'Westernised' and many now live in towns and have occupations similar to other local populations. The evolutionary origin of the Sami population has been an enigma. Archaeological sites in central and northern Sweden reveal the presence of people in this area as early as 9000 years before present (YBP). Among the first areas to become accessible after the last glaciation was the Atlantic coast of Scandinavia, and humans may have advanced along the Norwegian coastline and then moved inland towards Sweden and Finland. Humans may have also arrived at the Northern Shield through Finland from Western Eurasia or Continental Europe. Recent excavations in middle Sweden indicate that reindeer herding has existed for at least 1000 years and that the Sami population in this area is post-Medieval.3, 4 While humans may have arrived in the Northern Shield soon after the last glaciation, the relationship between those early settlers and the Sami people is not known. A total of 11 Sami dialects are recognised but only six of these are in common use with the remaining five being either extinct or spoken by less than 50 people. The Sami languages are members of the Finnic group, within the Finno-Ugric subfamily of the Uralic languages. Apart from the Sami, the Finnic group comprises languages from Finland and Estonia as well as the languages of several indigenous peoples from western Russia, including Udmurt, Mari and Komi, centred around the junction of the Volga and Kama rivers to the west of the Ural mountains. Early studies showed that the frequency of blood group and protein polymorphisms differ significantly between Sami and the general Swedish population5 and for some loci the data have been interpreted as indicative of an Asian influence.6 On the basis of classical markers, the Sami cluster with other Caucasian populations but as an outlier to Continental European populations.7, 8 Studies of multiple DNA markers have confirmed the overall similarity of Sami with other European populations,9 but some genetic markers yield results that are consistent with a genetic contribution from Asian populations,10 distinguishing Sami from the peoples of Southern and Western Europe. Y chromosome haplotypes have pointed to multiple founding lineages in both Finns and Sami and the Asian component in males has been estimated to be around 50%. Mitochondrial DNA (mtDNA) is frequently used for population studies. These studies have benefited from the fact that mtDNA is, for all practical purposes, clonally inherited and that it exhibits a high degree of polymorphism. Also, recent database resources enable comparisons of the pattern of genetic variation in the entire mtDNA genome in large population samples.11 Two mtDNA haplogroups (denoted V and U5b)12, 13 account for the majority of mtDNA diversity in Norwegian, Finnish and northern Swedish Sami, with a few other haplogroups (H, Z and D5) occurring at much lower frequencies.14 Haplogroup V is found across Europe and in low frequencies in Eastern European populations14 and has the highest frequency in Swedish (68%) relative to Finnish (37%) and Norwegian Sami (33%). Haplogroup U5b is present at low frequencies across Europe15 and shows the opposite trend with 26% in Swedish, 41% in Finnish and 57% in Norwegian Sami.14 The vast majority of Sami U5b sequences carry HVR-I (hypervariable region 1) substitutions at 16144, 16189 and 16270 which was referred to as the 'Sami-specific motif'8 or U5b115 haplogroup. Further, coding region variation has narrowed this designation down to U5b1b (ntps 7385 and 10927) and with the addition of the transition at 16144 the 'Sami-specific' subclade has been denoted U5b1b1.14 Haplogroup H is found at low frequency in the Sami relative to other Northern or Continental European populations.14, 16 Haplogroup H is the most common haplogroup in European populations and is present at low frequencies in Volga-Finnic populations and rare in central Asian populations.14, 17 The probable European origin and the higher frequency of H among Norwegian Sami suggests that haplogroup H entered Fennoscandia via a migration along the Atlantic coast of Norway or may be present in the Sami due to more recent admixture with European populations.14 The remaining haplogroups found at appreciable frequencies in Sami are D5 and Z.14 While D5 and Z are present at low frequencies in some Asian populations and D5 is relatively common in China,18 both are virtually absent in Europe, implying an Asian origin. Haplogroup Z is most frequent in Northeastern Asia19 and present in Siberian populations as well as in the Volga-Ural region.14 While subhaplogroup Z120, 21 has been observed in the Koryak and Itelmen populations,19 it has also been noted to account for all Z lineages in Western Asia and Northern Europe.14 The pattern of mtDNA haplogroup frequencies in the Sami indicates that the population may have been influenced by several migrations from different source populations. Previous studies of the mitochondrial DNA of the Sami have focused on haplogroup frequencies and estimates of genetic diversity based on HVR sequences. Here, we present an analysis of the complete mtDNA genome from the northern and southern Swedish Sami groups, with the purpose of studying the genetic structure of the populations and addressing the origin of the Sami people. mtDNA haplogroup frequenciesHaplogroups V (58. 6%) and U5b (35.5%) predominate in the northern Swedish Sami, with several other haplogroups (H, Z) occurring at low frequency (Table 1). This distribution is very similar to that presented previously for a population sample from this area, as well as to the distribution in Finnish and Norwegian Sami (Table 1).14 Haplogroups V and U5b are also present at high frequency in the southern Swedish Sami, along with haplogroups H, Z and a range of other haplogroups (Table 1). While the presence of V and U5b in both the northern and southern Swedish Sami at appreciable frequencies indicates that these two populations share the same genetic origin, the haplogroup distribution in the southern Swedish Sami population differs from the northern Sami in several respects. The frequency of haplogroups V and U5b is lower and haplogroup H (34.8%) much higher in the southern Swedish Sami. Also, the southern Swedish Sami have a number of other haplogroups not found in other Sami populations (I, J, K) but characteristic of Continental European populations (Table 1). The difference in haplogroup frequency distribution between southern Swedish Sami and the other Sami populations could be due to recent admixture with Swedish or other Continental populations. To further study these alternatives, we stratified the southern Swedish Sami sample into those with traditional occupations (ie reindeer herding) and those with nontraditional occupations, on the premise that those with traditional occupations are more likely to have exclusively Sami ancestors. The reindeer herders have a haplogroup distribution similar to that of northern Swedish Sami, with a lower frequency of haplogroup H and a higher frequency of V and U5b1b1 (Table 1). The southern Sami with nontraditional occupations have a haplogroup distribution similar to that of the Continental European population, with a high frequency of H and other 'non-Sami' haplogroups constituting more than 70%. The difference between these two groups of southern Swedish Sami could be due to admixture. Using the haplogroup frequencies for the northern Sami and Continental Europeans as the two source populations, we estimated the extent of admixture from the Continental European population in the combined southern Swedish Sami to be 48%, among those with traditional occupations to be 16% and among those with nontraditional occupations to be 67%, using the LEA software. Phylogeny of European and East Asian mtDNA lineagesTo study the relationship and genetic diversity within some of the mtDNA haplogroups in Sami populations, we sequenced complete Sami mitochondrial genomes from each of haplogroups V, U5b1b1 and Z and supplemented our dataset with published Sami sequences and complete sequences from other populations. Median-Joining networks were constructed for each of these haplogroups to study the relationship of the Sami mtDNA sequences and sequences from other populations. In the network for haplogroup V, Sami mtDNA sequences are scattered and mainly group with sequences from Finland (Figure 1a). Three of the Sami have identical sequences but there is no indication of monophyletic groups of Sami sequences. The network for haplogroup U5b contains representatives of the subhaplogroups U5b1b, U5b1b1, U5b1a, U5b1, U5b2 and U5b (Figure 1b). All Sami sequences are found in the U5b1b1 clade together with some sequences from Finland. The close relationship with sequences from Finland may be due to admixture.30 The nucleotide diversity for Sami sequences of haplogroups U5b1b1 and V is very low (pi=1 times 10-4 and pi=1.8 times 10-4, respectively). Calculated from the mean branch length to their shared node, the time to the most recent common ancestor of Sami haplogroup V sequences is 7600 YBP, and for U5b1b1 5500 YBP amongst Sami and 6600 YBP among Sami and Finns. The estimated ages of the U5b1b1 clades are in general agreement with an estimate of the age of their ancestral haplogroup (U5b1b) of 8600 YBP.31 Figure 1 - Median-Joining networks with relevant substitution positions based on the complete mtDNA genome sequences for individuals with haplogroups (a) V, (b) U5b and (c) Z. The networks have been constructed as described in the text. The colour coding is a follows: green – Sami; blue – Finland; red – Volga-Ural; orange – Continental Europe; pink – Japan; yellow – NE Asia; light blue – China; light green – India.The northern Swedish Sami have two dominating mtDNA haplogroups, similar to other Sami populations. The presence of these two haplogroups in all Sami populations, albeit at different frequencies, points to a common origin for all Sami populations in the northern Shield area. Among the Sami, the southern Swedish Sami are outliers in their distribution of mtDNA haplogroups. The high frequency of the haplogroups present in Continental Europe in the southern Swedish Sami with non-traditional occupations indirectly supports admixture with the (European) Swedish population. The admixture analysis confirms this observation, lending no support for the southern Swedish Sami having a different genetic origin than the northern Sami. The contemporary Swedish Sami population is estimated to number about 50 000 people,32 but the population size is likely to have been considerably smaller in historic times. The near complete dominance of only two haplogroups in the northern Swedish, Finnish and Norwegian Sami and the small population size indicates that the Sami could have been subject to strong genetic drift. This limited population size is supported by high linkage disequilibrium (LD) between microsatellite and SNP markers in Swedish Sami relative to the general population in Finland and Sweden.33, 34, 35, 36 The distribution of Sami lineages within the European haplogroup V indicates that Sami have been affected by a migration of Continental European tribes either moving directly north through Sweden or by way of the Atlantic coast, or alternatively, via the Volga-Ural region of Russia where V has been found at appreciable frequencies.14 Haplogroup U5b is widely dispersed in Europe and therefore provides few clues as to putative migrations. However, U5b1b1 has a restricted geographic distribution centred on Northern and Eastern Europe, where it has also been identified in the Volga-Ural region.14 The presence of haplogroup Z implies a contribution, albeit limited, to the Sami gene pool from Asia. The close relationship of Z1a lineages from Finns and Sami with those of the Volga-Ural again implicates that region as a probable source for Sami mitochondrial diversity. There is, however, a difference in the apparent ages of the different Sami haplogroups. The nucleotide diversity among Sami sequences for the three haplogroups studied here is very low. The ages of the variation for U5b1b1 and V among Swedish Sami are similar (5500 and 7600 YBP, respectively) but considerably older than for Z (2700 YBP). The surprisingly close link between haplogroup Z1a among Sami and the Volga-Ural sequences suggest that this haplogroup was brought in during the last 2–3000 YBP. Our data supports that a migration from Eastern Europe, in the vicinity of the Volga-Ural region, is the likely source for much of the Sami mtDNA diversity14 but indicates multiple migrations, the first being 6–7000 YBP and at least one additional migration 2–3000 YBP. Considering the similarity observed between Sami and Finnish mitochondrial lineages, this observation of multiple migration events would also support previous population genetic studies that have indicated dual origins of the Finnish people.37 Ingman, Max, and Ulf Gyllensten. " A recent genetic link between Sami and the Volga-Ural region of Russia." European Journal of Human Genetics 15.1 (2006): 115-120.
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Post by Admin on Mar 22, 2016 2:09:07 GMT
The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the “Saami motif” variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the “Saami motif,” was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found. mtDNA Analysis HVS-I was sequenced between nucleotide positions (nps) 16024 and 16383 of the revised Cambridge Reference Sequence (Andrews et al. 1999) in 73 Swedish Saami and 8,314 other mtDNA samples. RFLP analysis of diagnostic mtDNA positions was performed, and mtDNA haplogroups were assigned to each sample by use of published criteria (Torroni et al. 1992, 1994, 1996; Richards et al. 1998; Macaulay et al. 1999; Schurr et al. 1999; Finnilä et al. 2000, 2001; Herrnstad et al. 2002; Kivisild et al. 2002). In addition, all U5b genomes (n=160) from 31 populations were typed by sequencing for the np 5656 A→G mutation that differentiates between individuals belonging to haplogroups U5b* and U5b1. All identified U5b1 individuals (5656G) were further sequenced to assess the variation at nps 7385 (A or G) and 10927 (T or C). A summary of these data is given in table 4. Y-Chromosome Analysis Sixteen Y-chromosomal biallelic markers were assayed in 1,369 DNA samples. Nomenclature of haplogroups is as defined by the YCC (2002). Markers were analyzed as follows. The polymorphic SNPs underlying markers M52, M130 (RSP4Y), M170, M173, M178, M201 (Underhill et al. 2001), M269 (Cruciani et al. 2002), and M242 (Seielstad et al. 2003) were assayed after PCR amplification and sequencing. Markers M9, Tat, SRY-1532, 92R7, M89, and P43 were assayed through restriction digest analysis by use of published protocols (Mathias et al. 1994; Whitfield et al. 1995; Zerjal et al. 1997; Akey et al. 2001; Raitio et al. 2001; Karafet et al. 2002). The YAP and 12f2 polymorphisms were identified following the procedures of Hammer and Horai (1995) and Casanova et al. (1985), respectively. Furthermore, 35 Swedish Saami DNA samples that have previously been analyzed for Y-chromosomal variation by Rosser et al. (2000) were also typed in the present study for the biallelic markers M89, M52, M130 (RSP4Y), M170, M173, M178, M201, and M269 (YCC 2002). The phylogenetic network in figure 1 relates all the HVS-I sequence haplotypes in the three geographic subpopulations of the Saami. It also indicates a limited number of highly frequent haplotypes, which are, in most cases, shared by all analyzed geographic subpopulations (see table 2). Thus, 98% of the Saami mtDNA pool is encompassed within haplogroups V, U5b, H, Z, and D5. The two largest subsets, V and U5b, account for a lion’s share (89%) of the Saami mtDNA pool. The representative proportion of individual haplogroups varies substantially among different Saami subpopulations (table 2). Haplogroup V is by far the most frequent haplogroup in the Swedish Saami and is present at significantly lower frequencies (P<.0001) in Norwegian and Finnish subpopulations. We note that, in all three Saami subpopulations, U5b was virtually the only subclade of the otherwise frequent and divergent western Eurasian haplogroup U5 (Tambets et al. 2003). It is the most frequent haplogroup among Norwegian and Finnish subpopulations (table 2). Only a minor portion of the Saami maternal lineages (average ∼5%) that exhibit restricted diversity belong to haplogroups that are characteristic of Asian populations—that is, D5 and Z (table 1). These eastern Eurasian haplogroups are significantly more frequent (P<.05) among the Finnish Saami compared with Norwegian and Swedish Saami samples ( table 2). Such fluctuations in haplogroup frequencies could be due to genetic drift or just due to stochastic variation in relatively small samples. At the same time, the similar pattern of mtDNA haplogroup distribution found in different subpopulations of the Saami provides evidence of their common genetic background. The phylogeography and the ancestry of the other components of the Saami mitochondrial profile have so far not been well understood. Here, we showed that mtDNA haplogroup U5b1b1—the set of lineages with the so-called “Saami-specific” motif—is spread, besides among the Saami, mostly in eastern Europe (fig. 3B). This might suggest that haplogroup U5b1b1 may have spread/arisen from eastern Europe. On the other hand, the considerable diversity of the U5b1b cluster in western and southern Europe suggests that these regions, rather than eastern Europe, were the likely place of origin of U5b1b. Thus, the distribution of U5b1b is similar to that suggested above for haplogroup V. Notice that this cluster, like haplogroup V, is also found in northwestern Africa (table 4). Hence, we envision an initial diversification of U5b1b in western Europe, followed by the spread of a particular subhaplogroup in eastern Europe, finally reaching Fennoscandia (but not the Samoyeds or any other aboriginal Siberians) via an eastern route (fig. 4A). Indeed, U5b1b1 is absent from a large sample set of Germans from Lower Saxony (Pfeiffer et al. 2001), and it is detected only in trace frequencies in other western European populations. That makes it less likely that U5b1b1 entered the Saami mtDNA pool (or that the proto-Saami tribes carried it) directly from the west. The wide geographic distribution of both U5b1b1 and U5b1b in western Eurasian populations and the apparent absence of U5b1b “twigs” (except of U5b1b1) in Finno-Ugric speakers suggests that the latter may have originated before the differentiation of the European Finnic-speaking people. The two eastern Eurasian mtDNA variants, haplogroup Z1 and the particular subbranch of D5, have probably reached northeastern Europe not via the Arctic but via a more southern route across the southern Urals and, passing the Volga River basin (fig. 4A), left their “traces” among the gene pools of the Volga-Ural peoples, although not, as we have already stressed above, among Ob-Ugric and Nenets populations (table 1). Here, history and archeology provide several possible scenarios: not only events of historic times, like migrations of Huns, Avars, and Mongols, but also a likely influx of Asian tribes to eastern Europe during the early Holocene and contributing to the Kama culture of the upper Volga and Petchora basins (Kozlowski and Bandi 1984), could have been behind movements that brought a few selected and specific eastern Asian mtDNA variants to Fennoscandia. Note that northern Fennoscandia became accessible to humans at the very end of the Pleistocene/early Holocene, both from the west and the east (Donner 1995). The Y-chromosomal haplogroups N3 and R1a, which make up ∼60% of the Saami Y-chromosomal variants, have likely reached Fennoscandia from eastern Europe (fig. 4B), where these haplogroups can be found in high frequencies, as among the Saami. Haplogroups I and R1b, which together make up a third of Saami Y chromosomes, seem to have arisen in western Europe (fig. 4B). For R1b, this scenario is most plausible because it is a characteristically frequent Y-chromosomal variant in western Europe (table 3). In the case of haplogroup I, a specific pattern of STR variation in the Saami is close to that observed among other Scandinavians and western Europeans and is dissimilar to that observed in southern Europe. doi:10.1086/383203
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Post by Admin on Aug 4, 2016 21:25:47 GMT
Schematic reconstruction of possible entry routes of the predominant Saami maternal (A) and paternal (B) lineages to Fennoscandia. Broken lines indicate that the exact place of origin/route of spread of the haplogroup is unsolved/not indicated (Tambets et al. 2004). The Saami motif U5b1b1 entered Scandinavia 7,500 ybp and the Asian-specific haplogroup Z1 is associated with the appearance of the Kama culture ∼8,000 ybp. Haplogroup D5 arrived from East Asia after the Late Glacial Maximum (∼20,000 ybp), which preceded U5b1b1 and Z1. D5 and Z1 make up 16% in the Saami in Flnland today. The Saami with D5 and Z1 were the oldest settlers in Scandinavia, who were the brown-eyed, dark-haired people, and they admixed with U5b1b1 people from 7,500 ybp, which made them acquire European physical traits such as blond hair and blue eyes. Haplogroup U5 is the European hunter-gatherer haplogroup along with U4. Figure 1 Phylogenetic network of 445 Saami mtDNA HVS-I sequences. The phylogenetic network in figure 1 relates all the HVS-I sequence haplotypes in the three geographic subpopulations of the Saami. It also indicates a limited number of highly frequent haplotypes, which are, in most cases, shared by all analyzed geographic subpopulations (see table 2). Thus, 98% of the Saami mtDNA pool is encompassed within haplogroups V, U5b, H, Z, and D5. The two largest subsets, V and U5b, account for a lion’s share (89%) of the Saami mtDNA pool. The representative proportion of individual haplogroups varies substantially among different Saami subpopulations (table 2). Haplogroup V is by far the most frequent haplogroup in the Swedish Saami and is present at significantly lower frequencies (P<.0001) in Norwegian and Finnish subpopulations. We note that, in all three Saami subpopulations, U5b was virtually the only subclade of the otherwise frequent and divergent western Eurasian haplogroup U5 (Tambets et al. 2003). It is the most frequent haplogroup among Norwegian and Finnish subpopulations (table 2). The frequencies of the most widely spread haplogroups among the Saami in other analyzed populations are shown in table 1. Both haplogroups V and U5b are spread at moderate frequencies across Europe, from Iberia to the Ural Mountains. In contrast, among 393 Ob-Ugric speakers (including 98 Mansi, published elsewhere by Derbeneva et al. [2002b]) and 388 Samoyeds (including 58 Nenets, published elsewhere by Saillard et al. [2000]), only one haplogroup V–carrying individual was found in the Mansi sample, whereas not a single Saami variant of U5b (U5b1b1) was identified there (table 1). These two variants of maternal lineages are virtually absent in the other 1,199 native Siberians analyzed in this study. The third-most-frequent haplogroup among the Saami is H, which is present at a frequency of 4%, ∼10-fold lower than that of other North European populations (Richards et al. 2000). The majority of the Saami haplogroup H lineages (61%) contain transitions at nps 73 and 16162. According to information obtained from complete sequences, these lineages belong to subhaplogroup H1, defined by the coding region transition at np 3010 (Finnilä et al. 2001). We notice here that HVS-I haplotypes with a transition at np 16162 in the Volga-Ural area people (Bermisheva et al. 2002) and other European populations studied by us belong exclusively to this branch of subhaplogroup H1 (authors' unpublished data). This variant of mtDNA can be found both in western and eastern Europe, being as frequent in Germanic-speaking Scandinavians and the Germans as among the Norwegian Saami but absent in the Finnish and Swedish Saami (table 2). Though present in several Volga-Finnic populations, H1 haplotypes with mutation 16162 are extremely rare or absent in almost 2,000 Siberian Ugric-, Samoyedic-, and Altaic-speaking people (table 1) as well as in central Asians (Comas et al. 1998; Metspalu et al. 1999)—that is to say that this clade has an overwhelmingly European phylogeographic pattern. Its presence only in the Norwegian Saami sample may have been generated by admixture with the Norwegian population. This inference is supported by the presence of one H1 haplotype, with HVS-I motif 16162–16189, found among the Saami, in the Norwegian sample (Helgason et al. 2001). This haplotype has not been found in any other population analyzed in the present study. Only a minor portion of the Saami maternal lineages (average ∼5%) that exhibit restricted diversity belong to haplogroups that are characteristic of Asian populations—that is, D5 and Z (table 1). These eastern Eurasian haplogroups are significantly more frequent (P<.05) among the Finnish Saami compared with Norwegian and Swedish Saami samples (table 2). Such fluctuations in haplogroup frequencies could be due to genetic drift or just due to stochastic variation in relatively small samples. At the same time, the similar pattern of mtDNA haplogroup distribution found in different subpopulations of the Saami provides evidence of their common genetic background. Phylogeography of Haplogroup U5b1b and the “Saami-Specific” Motif (U5b1b1) Haplogroup U5b is found at low frequencies all over Europe (Richards et al. 1998). A distinct phylogenetic subbranch of U5b carries the “Saami-specific” HVS-I motif defined by 16144-16189-16270 in the study by Sajantila et al. (1995) and has been named “U5b1” by Richards et al. (1998). All U5b sequences share two diagnostic synonymous substitutions at nps 7768 and 14182 (see fig. 3A). The major U5b subset found among the Finns contains a derived G allele at noncoding np 5656 and a synonymous substitution at np 12618 (Finnilä et al. 2001). Through use of complete mitochondrial sequence data, it has previously been demonstrated that the Finnish sequences containing the “Saami-specific” HVS-I motif share an additional synonymous mutation at np 10927, which is often associated with another transition at np 7385 (Finnilä et al. 2001). To study the phylogeography of the “Saami-specific” branch of U5b, an analysis of np 5656 variation among the relevant genomes was performed. The results reveal (see table 4) that 95 of 160 samples carried the derived 5656G allele and belong, thus, to a subhaplogroup referred to as “U5b1.” We note that this subhaplogroup is different from the U5b1 branch defined by Richards et al. (1998) using HVS-I data alone. Here, “U5b1” refers to a deeper phylogenetic node of U5b (see fig. 3A). The transition at np 7385 was always found to be associated with a transition at np 10927 and is referred to as “U5b1b.” This cluster also includes the “Saami-specific” subclade, which we name here as “U5b1b1” (fig. 3). Notice that the sequence motif 16189-16192-16270 in U5b1 appears to be associated with at least three independent subhaplogroups of U5b: U5b* (5656A), U5b1*/U5b1a (5656G, 7385A, and 10927T), and U5b1b (5656G, 7385G, and 10927C) (fig. 3; table 4). Therefore, reliance on published HVS-I sequences alone, without regard to the relevant coding region information, makes the exploration of the phylogeography of haplogroup U5b1b ambiguous, and these sequences were not included in the analysis. The 5656G allele, including all major subsets of U5b1, is broadly distributed both in western and eastern Europe (fig. 3A; table 4). The U5b1b subclade is found all over Europe, but it occurs in western and central Europe with notable sequence variation. The haplotype diversity (excluding subclade U5b1b1) is 0.96. We note that U5b1b was also identified in a northwestern African population, among the Moroccans (fig. 3A). In contrast, its diversity in eastern Europe is much lower. There, the haplotype diversity (excluding subclade U5b1b1) is 0.79, whereas most of the U5b1b sequences in eastern Europe belong to the U5b1b1 branch (fig. (fig.3A3A and and3B).3B). In the Eurasian cohort, U5b1b (other than U5b1b1) is absent from native Siberians and is notably absent from the Ob-Ugric populations and the Samoyeds. Most importantly, the data indicate that U5b1b1, the only subcluster of U5b in the Saami population, is present outside the Scandinavian-Baltic and the Volga-Uralic regions—namely, in the French, Croatian, Bosnian, Slovenian, Czech, Russian, Ukrainian, Polish, and Hungarian mtDNA pools—and, further, is present even in the Caucasus, among the Nogay, Kabardinian, and Armenian mtDNAs (fig. 3B). Thus, this subhaplogroup is much more widely distributed than was believed previously (Sajantila et al. 1995). Two principal haplotypes, differing by one mutational step, define the Saami U5b1b1 (fig. 3B). One, with transitions at nps 16144, 16189, and 16270, can be identified as the founder haplotype because of its presence in many other populations. The second, containing an additional transition at np 16148, is so far exclusive to the Saami population. This subfounder comprises 38% of their U5b1b1 mtDNAs and is present in all studied subpopulations of the Saami. Furthermore, no other derivatives of the U5b1b1 founder node present in the Saami sample was identified in other Scandinavians, including the Finns, irrespective of the previous observation that the northern-central Finnish population is relatively rich in U5b1b1 (Meinilä et al. 2001). Thus, the “leakage” of the Saami U5b1b1 to neighboring populations seems to be rather limited. The coalescence time of all non-Saami U5b1b1 lineages in Europe (see fig. 3B) is 4,300±1,400 years BP (table 5). This is approximately the same as that for the eastern or western-southern European subsets but is older than that observed for Scandinavians. Am J Hum Genet. 2004 Apr; 74(4): 661–682.
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Post by Admin on Aug 5, 2016 21:23:30 GMT
The absence of strong structure in the present-day mtDNA gene pool of NEE stands in contrast to the variety of languages and cultures, and to the complex history of how and when these were formed. Modern mtDNA data does not resolve the origins of the Saami either. Our aim was to provide answers to these questions and reconstruct events in the genetic history of NEE by generating and analyzing ancient DNA (aDNA) data from prehistoric human remains collected in northwest Russia (Figure 1). In particular, our objective was to characterize the genetic relationships between hunter-gatherer populations in NEE and Central/Northern Europe and to estimate the genetic legacy of ancient populations to present-day NEE and Saami. The oldest samples were collected in the Mesolithic graveyards of Yuzhnyy Oleni Ostrov (aUz; ‘Southern Reindeer Island’ in Russian) and Popovo (aPo), both dated around 7,000–7,500 uncalibrated. yBP, uncal. yBP. The sites of aUz and aPo are located along one of the proposed eastern routes for the introduction of Saami-specific mtDNA lineages [32]. Results from odontometric analyses suggested a direct genetic continuity between the Mesolithic population of Yuzhnyy Oleni Ostrov and present-day Saami [41]. We also analyzed human remains from 3,500 uncal. yBP site Bol'shoy Oleni Ostrov (aBOO; ‘Great Reindeer island’ in Russian) in the Kola Peninsula. This site is located within the area currently inhabited by the Saami. We compared the ancient mtDNA data from NEE with a large dataset of ancient and modern-day Eurasian populations to search for evidence of past demographic events and temporal patterns of genetic continuity and discontinuity in Europe. In order to identify the genetic affinities of the two ancient populations with other ancient and present-day Eurasian populations, mtDNA hg distributions were compared by Principal Component Analysis (PCA). The PCA plot of the first two components (41.5% of the total variance, Figure 2) showed that present-day populations largely segregate into three main clusters: Europeans (in yellow), Middle Easterners (in grey) and Central/East Siberians (in blue). The spread of extant populations of Europe and Central/East Siberia along the first component axis (28.5% of the variance) appeared to reflect their longitudinal position, whereas Europeans and Middle Easterners were separated along the second component axis (13.0% of the variance). As shown previously, populations of the ‘Central/East Siberian’ cluster were predominantly composed of hgs A, B, C, D, F, G, Y, and Z, while in contrast populations of the ‘European’ cluster were characterized by higher frequencies of hgs H, HV, V, U, K, J, T, W, X, and I (e.g., [43]–[47]). The two ancient groups - aUzPo and aBOO - from two individual time periods appeared remarkably distinct on the basis of the PCA, suggesting a major genetic discontinuity in space and time. The hg distribution in the Mesolithic aUzPo population: U4 (37%), C (27%), U2e (18%), U5a (9%), and H (9%), indicated an ‘admixed’ composition of ‘European’ (U4, U2e, U5a and H, 73%) and ‘Central/East Siberian’ (C, 27%) hgs, based on the PCA plot (Figure 2). Interestingly, the population of aUzPo did not group with modern NEE populations, including Saami, but fell instead between the present-day ‘European’ and ‘Central/East Siberian’ clusters on the PCA graph, and more precisely between populations of the VUB (in light green) and West Siberia (in dark green). The high frequency of hg U4 is a feature shared between Mesolithic aUzPo, present-day VUB (Komi, Chuvashes, Mari), and West Siberian populations (Kets, Selkups, Mansi, Khants, Nenets), with the latter group also being characterized, like aUzPo, by the presence of hg C. The genetic affinity between Mesolithic aUzPo and present-day West Siberian populations could be visualized on the genetic distance map of North Eurasia (Figure 3A), on which locally lighter colorings indicated low values of genetic distances, and therefore an affinity between aUzPo and extant West Siberians. Comparison of 3,500 uncal. yBP Bol'shoy Oleni Ostrov (aBOO) with extant populations of Eurasia At the 3,500 uncal. yBP site of aBOO, we observed 39% ‘European’ hgs: U5a (26%), U4 (9%), T (4%), and 61% ‘Central/East Siberian’ hgs: C (35%), Z (13%), D (13%). Concordant with this admixed hg make-up, PCA indicated a position close to present-day Siberians (Figure 2). This position did not change when potential maternal relationships among individuals were accounted for by excluding redundant haplotypes (Figure S2B). The genetic relationship between aBOO and Siberians was also evident on the genetic distance map, where the area representing the lowest genetic distance covered a broader area of Siberia than for aUzPo (Figure 3B). The extant populations that showed most genetic similarity to aBOO were found in Central and East Siberia. In contrast, the area of maximum similarity for aUzPo lay in West Siberia (Figure 3A); this observation however could be influenced by low sample size in aUzPo. Haplotype sharing analyses for aBOO confirmed the genetic affinity with modern-day West and Central/East Siberians inferred from the PCA (Figure 4), but also identified a close relationship with the VUB population pool. The distribution of haplotype matches observed in pools of the VUB, West Siberia and Central/East Siberia was partly due to the presence of basal C* (16223T-16298C-16327T) and D* (16223T-16362C) haplotypes in these pools, whereas these types were absent in Middle Eastern and European pools. Central Siberian Tuvinians displayed the highest percentage of shared haplotypes with aBOO (12.2%) although all shared haplotypes belong to hgs C* and D*. A more explicit genetic link between aBOO and extant East Siberians was seen in the presence of the derived C5 haplotype (16148T-16223T-16288C-16298C-16311C-16327T) in aBOO and in one single Buryat individual of Central Siberia [54]. The Z1a haplotype (16129A-16185T-16223T-16224C-16260T-16298C) detected in aBOO had a broad but interesting distribution in Eurasia. It was found in all Central/East Siberian pools except in Tuvinians, but also in the Bashkirs of the Urals, in the VUB pool, as well as in Scandinavian and Baltic populations (Norwegians, Swedes, Finns, Ingrians, Karelians, and the Saami). Although haplotype sharing analyses revealed genetic links between aBOO and extant populations of NEE, a strong genetic differentiation was obvious between aBOO, modern-day NEE and Saami. This genetic discontinuity was further supported by BayeSSC analyses (Figure 5; Table 3). Similarly to aUzPo, a better fit was obtained for the model involving a 10% migration from CE over the last 3,500 years (H1b; ω = 1.00E+0) than for the model of genetic continuity between aBOO and NEE (H0b; ω = 3.86E-10). Comparison among ancient Eurasian populations Previously described populations of hunter-gatherers of Central/East Europe (aHG [12], [14]) and Scandinavia (aPWC, [13]) were characterized by high frequencies and diversity of hg U4, U5a and U5b, which caused the two ancient datasets to group outside the cluster of extant European populations on the PCA plot (Figure 2). This matches previous studies that have shown that genetic continuity between hunter-gatherers and present-day Europeans can be rejected [12]–[13]. Like other European hunter-gatherers, aUzPo is characterized by high frequencies and diversity of hgs U4 and U5, but was genetically differentiated from aHG and aPWC due to the occurrence of hg C. Despite the fact that high frequencies of hgs U5b and V cluster the aHG and aPWC hunter-gatherer groups on the PCA plot (Figure 2), and that these hgs are also common in modern-day Saami, the ‘Saami motif’ is absent from aPWC and genetic continuity between aPWC and modern-day Saami was rejected [13]. Although the aBOO individuals were also characterized by high frequencies of hg U, the group appeared less close to the Palaeolithic/Mesolithic hunter-gatherers aHG and aPWC on the PCA plot than aUzPo. Haplotype sharing analyses (Figure 6) also showed that aBOO shared less haplotypes with aHG and aPWC than aUzPo (4.76% and 0.00%, respectively, versus 9.52% and 36.84%). This observation was confirmed by the analyses of our coalescent simulations, in which a model of genetic continuity between aHG, aPWC and aUzPo (ω = 9.91 E-1; H0d) was better supported than a model of genetic continuity between aHG, aPWC and aBOO (ω = 1.10 E-4; H0e). As demonstrated above, aBOO exhibited greater genetic affinities with extant populations of Siberia than aUzPo. Accordingly, aBOO shared more haplotypes with ancient samples from Siberia aEG (10.87% [55]) and aKUR (7.69% [56]) than aUzPo (0.00% and 7.69%, respectively; Figure 6). Percentages of haplotypes from aUzPo and aBOO matched in selected ancient Eurasian populations. The present-day Saami populations display clear haplotypic differences from all the ancient populations sampled for DNA so far (prehistoric hunter-gatherer populations of North/South/Central/East Europe, aUzPo and aBOO) where none of the hg V and U5b1b1a lineages distinctive of the Saami could be detected. We show here that the mitochondrial ancestors of the Saami could not be identified in the ancient NEE populations of aUzPo or aBOO, despite the latter site being within the area occupied by Saami today. The widespread modern-day distribution of U5b1 and V lineages makes it difficult to identify the origins of the Saami [32]. Sub-haplogroup U5b1b1 to which the ‘Saami motif’ belongs was proposed to have originated and spread from southern/central Europe after the Late Glacial Maximum [32]–[33]. Despite its clear association with Saami ancestry, the ‘Saami motif’ also occurs at low frequency (below 1%) in a wide range of non-Saami populations in Europe, and haplotypes closely related to the ‘Saami motif’ have even been found in modern Berbers of North Africa [33]. Two origins have been proposed on the basis of archaeological and genetic evidence [24], [32]. First, ancestors of the Saami were suggested to have reached Fennoscandia from Western Europe along the Atlantic cast of Norway as part of the expansion of Mesolithic post-Ahrensburgian cultures (Fosna-Hensbacka and Komsa) in the early Holocene (∼10,000–11,000 yBP). Alternatively, the Saami were proposed to find their origins in Mesolithic post-Swiderian cultures (Kunda, Veretye, Suomusjärvi), which had moved from Poland into NEE also in the early Holocene [24]. The data from aUzPo, in which neither U5b1 or V could be detected, does not support the latter hypothesis. If migrations brought U5b1 and V to Fennoscandia from the East, they must have occurred after 7,500 yBP or have had a weak genetic impact on surrounding populations of NEE. Saami mtDNA diversity has been influenced by a combination of founder event(s), (multiple) bottlenecks, and reproductive isolation, which are likely due to the challenging conditions of life in the subarctic taiga/tundra [32]. The complex demographic history of Saami renders their population history difficult to reconstruct on the basis of modern genetic data alone. Further temporal population samples will be required, especially along the proposed alternative western migration route into sub-arctic Europe.
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