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Haplogroup R0 (mtDNA)

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Haplogroup R0
Possible time of origin	23,600 to 54,900 YBP^[1]
Possible place of origin	Near East or South Asia
Ancestor	R
Descendants	HV, R0a
Defining mutations	73, 11719^[2]

In human mitochondrial genetics, Haplogroup R0 (formerly known as Haplogroup pre-HV^[3]) is a mitochondrial DNA (mtDNA) haplogroup.

Origin

Haplogroup R0 derives from the macro-haplogroup R. It is an ancestral haplogroup to R0a and Haplogroup HV (and therefore to Haplogroup H and Haplogroup V).

Distribution

Haplogroup R0 occurs frequently in the Arabian Plate with its highest frequency in Socotri (Population 50,000 Yemen) 38% ^[4] and its also found in a high frequency in the Kalash (Population 6,000 in Pakistan) with 23%^[5] smaller frequency in North Africa, the Horn of Africa, Anatolia, Iranian Plateau & Dalmatia. Its greater variety in the Arabian Plate suggests R0a originated in and spread from there.

Subclades

Tree

This phylogenetic tree of haplogroup R0 subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation^[2] and subsequent published research.

R
- R0 or pre-HV
  - R0a or (preHV)1
    - R0a1 or (preHV)1a
      - R0a1a
    - 60.1T
      - R0a2 or (preHV)1b
        
        R0a2a
        
        R0a2b
        
        R0a2c
        
        R0a2d
        
        R0a2e
    - HV
      - HV0
      - HV1
      - 73
      - HV4
      - HV5
      - H

References

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Internal Diversification of Mitochondrial Haplogroup R0a Reveals Post-Last Glacial Maximum Demographic Expansions in South Arabia

+ Author Affiliations

¹Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, The Czech Republic
²Department of Anthropology, University of Florida, Gainesville
³Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
⁴General Department of Forensic Sciences & Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
⁵Laboratoire d’Anthropogénétique, Départment de Biologie, Université Chouaïb Doukkali, El Jadida, Morocco
⁶Laboratory of Genetics Immunology and Human Pathology, Faculty of Sciences of Tunis, Tunis, Tunisia
⁷Department of Clinical Biochemistry, Faculty of Medicine and Health Sciences, University of Sana’a, Sana’a, Yemen
⁸Faculdade de Medicina da Universidade do Porto, Porto, Portugal

*Corresponding author: E-mail: cerny@arup.cas.cz

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Abstract

Widespread interest in the first successful Out of Africa dispersal of modern humans ∼60–80 thousand years ago via a southern migration route has overshadowed the study of later periods of South Arabian prehistory. In this work, we show that the post-Last Glacial Maximum period of the past 20,000 years, during which climatic conditions were becoming more hospitable, has been a significant time in the formation of the extant genetic composition and population structure of this region. This conclusion is supported by the internal diversification displayed in the highly resolved phylogenetic tree of 89 whole mitochondrial genomes (71 being newly presented here) for haplogroup R0a—the most frequent and widespread haplogroup in Arabia. Additionally, two geographically specific clades (R0a1a1a and R0a2f1) have been identified in non–Arabic speaking peoples such as the Soqotri and Mahri living in the southern part of the Arabian Peninsula where a past refugium was identified by independent archaeological studies. Estimates of time to the most recent common ancestor of these lineages match the earliest archaeological evidence for seafaring activity in the peninsula in the sixth millennium BC.

Key words

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Introduction

During the course of the past 10 years, the study of the first migration of anatomically modern humans Out of Africa through the Bab el-Mandab Strait has dominated both archaeological (Petraglia and Alsharekh 2003) and genetic (Quintana-Murci et al. 1999; Kivisild et al. 2004; Macaulay et al. 2005) investigations of the Arabian Peninsula. Consequently, this issue has overshadowed other periods of prehistory that might have been even more significant in the formation of regional extant population.

In particular, recent archaeological and palaeoclimatological investigations have revealed the importance of the terminal Pleistocene and Holocene in the population history of Arabian Peninsula (Petraglia and Rose 2009) and have identified three possible core zones (the Red Sea, the South Arabian [Dhofar], and the Persian Gulf Basins) that could have served as refugia during environmental downturns (Rose and Petraglia 2009). It appears that the period from 35 to 20 thousand years ago (henceforth referred to as KYA), as lake deposits in northern and southern parts of the Peninsula testify, was a favorably wet one. Subsequently, however, the Last Glacial Maximum (LGM), a period lasting several thousand years from around 20 KYA, has been marked by eolian processes (erosion and deposition caused by wind) and dune formation in the Rub’ al Khali desert as well as other places of Arabia (Bailey 2009; Parker 2009). This change to a harsher and more arid climate was likely associated with the general movement or exodus of hunter–gatherer populations to more hospitable locations.

New evidence points to a brief additional wet phase between 15 and 13 KYA (Parker 2009). This could be related to the Bölling-Allerød (BA) interstadial (dated also between 15 and 13 KYA), which, in the northern latitudes, is associated with the mass wasting of its ice sheets. According to Parker (2009), “The BA brief interlude may have permitted brief human entry into parts of Arabia either from outside the peninsula or from refugia within Arabia (e.g., Dhofar or the now submerged Arabo-Persian Gulf Basin).” The most suitable places for population concentration were regions with high altitudes, which still today bear the highest population densities (Wilkinson 2009). The onset of the Younger Dryas ∼13.5 KYA ended the climatically favorable period until the Early Holocene when monsoon precipitation again increased ∼9.0 KYA. This last pluvial phase lasted until ∼5.0 KYA when present climatic conditions were established (Parker 2009).

Archaeological research has revealed that southwest Arabia, especially the highlands, must have been well populated over the past 5,000–6,000 years and may have acted as a long-term population centre during much of the Holocene (Wilkinson 2009); it remains to be determined if it also acted as a refuge for populations during the Palaeolithic. Furthermore, phylogenetic analyses of linguistic data demonstrate an expansion of extant Semitic languages throughout southern Arabia and East Africa some 1,000–3,000 years ago and their initial entry into the region may have occurred thousands of years earlier (Kitchen et al. 2009).

The contemporary distribution of ancestral and derived mitochondrial DNA (mtDNA) sequences shows that modern human colonization of Eurasia may have been accomplished via a southern coastal route ∼60–80 KYA (Forster et al. 2001; Metspalu et al. 2004; Macaulay et al. 2005; Thangaraj et al. 2005). Subsequent mtDNA diversification took place in south-western Asia, where haplogroups M and N (and its derivative R) evolved. In fact, precisely where these lineages first emerged is still under discussion. According to Metspalu et al. (2004), this process took place in three distinct regions in southern Asia (the Middle East, the Indus Valley, and East Asia) with only minor migrations between these regions. One of the most important results of such past mtDNA diversification processes is the absence or very low frequency of M haplogroups in Western Eurasia today, demonstrating that the division of an original “Out of Africa” gene pool can be placed somewhere west of the Indus Valley, with a later westward migration to the Middle East and back to Africa including only subbranch M1 (Forster et al. 2001; Olivieri et al. 2006).

Given its recent elevation to pivotal location in terms of past human migrations, the Arabian Peninsula became the focus of several genetic studies, both for mtDNA and for Y-chromosome markers (Richards et al. 2003; Kivisild et al. 2004; Luis et al. 2004; Abu-Amero et al. 2007; Rowold et al. 2007; Abu-Amero et al. 2008; Cadenas et al. 2008; Černý et al. 2008, 2009; Alshamali et al. 2009). At the mtDNA level, great complexity of the South Arabian gene pool has been demonstrated as gene flow from Eurasia for a substantial proportion of Ethiopian and Yemeni mtDNA haplotypes, especially (preHV)1 (Richards et al. 2003; Kivisild et al. 2004). Furthermore, Saudi Arabian mtDNAs show a high frequency of (preHV)1 lineages and molecular dates of main branches of this haplogroup fall within the Early Holocene (Abu-Amero et al. 2007, 2008; even if confidence intervals were large due to the small number of sequences).

The importance of the (preHV)1 haplogroup, recently renamed R0a (Torroni et al. 2006), was further demonstrated in a regional study of four Yemeni populations where a high level of sharing of R0a sequences was particularly striking given the otherwise low levels of haplotype sharing across Yemen (Černý et al. 2008). Moreover, it has been found that R0a is not only frequent but also diversified on Yemen’s Soqotra Island, where the new branch R0a1a1 has recently been identified (Černý et al. 2009).

Due to the high frequency of the R0a haplogroup and its internal diversification within Arabia and neighboring regions, we have focused our attention on this specific branch of mtDNA phylogeny. We present 71 new R0a whole-genome sequences from southern Arabia (Yemen) and northern/Horn of Africa (Somalia, Ethiopia, Sudan, Tunisia, and Morocco). These new sequences, together with 18 previously published genome sequences, reveal phylogeographic differences in the regional distribution of R0a throughout the Arabian Peninsula and East Africa. Estimations of the time to the most recent common ancestor (TMRCA) for different R0a subbranches, calculated with recently updated substitution rates, are discussed in the light of archaeological and paleoclimatic data.

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Materials and Methods

Samples

Yemeni R0a haplotypes came from two different sampling collections undertaken by two authors (V.C. and C.M.). Those (n = 22) from the V.C. Yemeni data set (n = 250) were published recently and their locations are described therein (Černý et al. 2008, 2009). The Yemeni data set of C.M. (n = 550), from which we have used 28 R0a haplotypes, come from highland areas (Dhamar, Amran, Hajja, and Taizz), lowland areas near the Red Sea (Zabid), desert areas (Al Bayda, Abyan, Jawf, Maarib, and Shabwa), and the eastern part of Yemen (Hadramawt and Al Mahra). We also performed complete mtDNA sequencing on one Ethiopian Jewish R0a haplotype from the collection of C.M. In addition, we surveyed our Central, East, and North African data sets for the presence of R0a haplotypes, resulting in 2 samples out of 448 Chad Basin samples (Černý et al. 2007), 4 samples out of 149 from Somalia (unpublished), 4 out of 77 from Ethiopia (unpublished), 4 out of 102 from Sudan (unpublished), 4 out of 304 from Tunisia (Cherni et al. 2009), and 2 out of 81 from Morocco (Harich et al. 2010). In total, 71 haplotypes were selected for complete genome analysis (see supplementary material 1, Supplementary Material online).

Laboratory Work

Amplification of the hypervariable segment 1 (HVS-1) of samples from the V.C. data set was reported previously (Černý et al. 2008, 2009). Amplification of HVS-1 of the C.M. data set was performed using primer pair P23 (Gonder et al. 2007). From the combined set of HVS-1 sequences, we classified R0a haplotypes as those displaying substitutions at positions 16126 and 16362 and clearly not ascribed to any other haplogroup, such as J (which has an additional substitution at position 16069) or T (which also has a substitution at position 16294).

Whole-genome sequencing of all Yemeni, Chad, and Ethiopian Jew (total 53) samples was conducted using 24 primer pairs (Gonder et al. 2007). In contrast, 18 samples from Somalia, Ethiopia, Sudan, Tunisia, and Morocco were analyzed using 32 primer pairs (Maca-Meyer et al. 2001; Pereira et al. 2007). Polymerase chain reaction (PCR) products were purified and sequenced using the forward primers only. However, in cases of the poly-C stretch between nucleotides 568–573 and 16184–16193, the reverse primers were used as well. Sequencing was performed on an ABI 3100 DNA Analyzer (Applied Biosystems, Foster City, CA). Chromatograms were evaluated by two independent observers (V.C. and L.P.) with the help of SeqScape (Applied Biosystems) and BioEdit version 7.0.4.1 (Hall 1999). In cases of ambiguous results, new PCR amplification and sequencing reactions were performed. The complete mtDNA sequences are deposited in GenBank database with accession numbers: HM185203–HM185273.

Phylogenetic Analyses

A preliminary reduced median network analysis (Bandelt et al. 1995) led to a suggested branching order for the tree, which was then constructed by hand. All variable positions were used except 16182C, 16183C, and 16519, as they are too recurrent and inconsistently reported in the literature. We compared our phylogenetic reconstruction with the trees published in two papers (Abu-Amero et al. 2007; Alvarez-Iglesias et al. 2009) and found the only differences to be in the placement of the highly recurrent substitution at position 58 and the insertion 60.1T (for which we used the most parsimonious inference), and in the nomenclature of some branches due to updated information in our expanded phylogeny.

We used 71 new Yemeni, Moroccan, Tunisian, Sudanese, Ethiopian, Somali, and Chad whole R0a genome sequences and 18 previously published whole R0a genome sequences (Achilli et al. 2004; Palanichamy et al. 2004; Abu-Amero et al. 2007; Gasparre et al. 2007; Behar et al. 2008; Costa et al. 2009; Hartmann et al. 2009). An inconsistency was detected between the sequences deposited in GenBank and the tree published in Abu-Amero et al. (2007) for position 16355, which was reported as a transversion to A in GenBank and a transition in the published tree; we decided to consider it as the transition as it seems to be the most probable variant when compared with other genome and HVS-1 sequences. For calculation of the TMRCA for specific clades in the phylogeny, the ρ statistic (mean divergence from inferred ancestral haplotype) was used with mutation rate estimates for complete sequence of one substitution in every 3,624 years corrected for the effect of purifying selection and for the synonymous substitutions of one substitution in every 7,884 years (Soares et al. 2009) using the calculator provided in that paper. Standard errors were calculated as in Saillard et al. (2000).

Interpolation Maps and Evaluation of Spatial Autocorrelation

To determine and visualize the geographical distribution of R0a and R0a1a, interpolation maps were drawn using the “Spatial Analyst Extension” of ArcView version 3.2 (www.esri.com/software/arcview). The “inverse distance weighted” (IDW) option with a power of two was used for the interpolation of the surface. IDW assumes that each input point has a local influence that decreases with distance. The geographic location used is the centre of the distribution area from where individual samples of each population were collected. This allows one to obtain the Morans I index and Z score (a statistic that assesses the significance of the null hypothesis, H0: there is no spatial pattern among the values associated with the geographic points in the study area). Correlograms for Morans I indices versus distances were obtained for R0a and R0a1a haplogroups using PaSSAGE software v 1.0 (www.passagesoftware.net). An interval of ten distance classes was used for all data points studied here and compared with ten distance classes for fewer data points (grouping some of the closest Yemen samples). The existence of a cline is assumed when a continuous decline trend composed of statistically significant points is observed.

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Results

Frequencies and Geographic Distribution of R0a Haplogroups

In our population data sets of 800 HVS-1 sequences from Yemen, 176 samples (22%) were classified as R0a comprising 46 different haplotypes. The ancestral type, with only two diagnostic variants present in HVS-1 (16126–16362), is the most common (n = 43). This haplotype is present in 16 of 22 different Yemeni populations (see supplementary material 2, Supplementary Material online). The second most common haplotype (n = 38) is a one step descendant of the ancestral type (16126-16355-16362), which has been named R0a1a (Abu-Amero et al. 2007; Černý et al. 2009). These two haplotypes constitute almost half of the R0a pool in Yemen.

Among the next most frequent R0a haplotypes, R0a1a1a (16126-16172-16355-16362), previously identified only in Soqotra (Černý et al. 2009), was also observed in Al Mahra, the region of eastern Yemen near Omani Dhofar close to Soqotra. A similar frequency, but much wider geographical distribution, was also noted for haplotype 16126-16304-16362. The rest of the R0a haplotypes (n = 42) had quite low frequency, occurring mostly in only one of the sampled populations (see supplementary material 2, Supplementary Material online).

The geographic distribution of R0a frequencies was plotted across the Arabian Peninsula and neighboring regions. Figure 1a shows the highest frequency of R0a on Soqotra Island and the neighboring territory of Al Mahra, where it is observed in approximately one-third of the samples. Other locations in Yemen and Saudi Arabia show lower frequencies of R0a (except for some points near the Red Sea and in the central region of Saudi Arabia). Radiating from the main highest R0a frequency focus, frequencies decrease in all directions. The global value of Moran’s I index (Moran’s I index = 0.06; Z score = 1.9 standard deviations) shows that there is a 5–10% likelihood that this clustered pattern is the result of random chance. The plot of R0a1a is shown in figure 1b, and the global value of Moran’s I index (Moran’s I index = 0.01; Z score = 0.87 standard deviations) suggests that this pattern is random. The distribution of Moran’s I index versus distance classes (fig. 2a and b) shows that the distribution of both haplogroups is clinal, although some values of the distances classes are not statistically significant.

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FIG. 1

Interpolation maps for R0a (a) and R0a1a (b) haplogroups.

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FIG. 2.

Spatial autocorrelation analyses for R0a (a) and R0a1a (b) haplogroups; filled points are statistically significant at the 5% level.

R0a Phylogenetic Tree Based on Whole-Genome Information

The R0a tree now includes 89 individuals, 71 of which are complete new sequences. Whole-genome sequencing revealed several coding region mutations important for the R0a topology. Figure 3 shows a simplified version of the R0a tree but the tree in the supplementary material 3 (Supplementary Material online) lists all mutations and all samples.

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FIG. 3.

Main branches of the complete R0a mtDNA tree. The boxes with the haplogroup names are placed at the level of the respective TMRCA.

As was shown before (Abu-Amero et al. 2007), there are two main R0a branches, designated R0a1 and R0a2. R0a1 is defined by one substitution at position 827 and the largest proportion of its haplotypes, as explained in the previous section, bear substitutions at positions 146-8292-11761-16355 and form the previously named haplotype R0a1a. Most of the branches in R0a1a derive from the root. All Soqotra samples and one Tunisian sample belonging to this haplogroup share a substitution at position 13708; eight out of nine of these samples, and one sample from Al Mahra, share an additional substitution at position 16172, which we previously identified as haplogroup R0a1a1a (Černý et al. 2009). Thus, it seems that R0a1a1 may be widespread in Yemen but rare elsewhere, whereas R0a1a1a is dominant in Soqotra and only appears in geographically close areas.

Haplogroup R0a2 (bearing an insertion at position 60 and substitutions at 2355-15674) also shows several branches deriving directly from the root, but it contains a much larger number of subclades. Some of these subclades were previously named by Alvarez-Iglesias et al. (2009), but the improved resolution of our tree supports some revisions in nomenclature (see supplementary material 3, Supplementary Material online). An interesting branch is the widespread R0a2f. It was characterized by a substitution at position 8251, which was observed in one Italian and two nomadic Arabs from Chad. Further derived R0a2f haplotypes were observed in a cluster of eight Yemeni sharing substitutions at positions 131-7837-12542-13708-13827. This R0a2f1, without identifying mutations within the HVS-1 region, and for that reason not previously recognized (Černý et al. 2009), is also specific to Soqotra and adjacent regions of Yemen (four haplotypes were found on Soqotra, three in Al Mahra, and one in Hadramawt).

Furthermore, we detected a new branch diverging from the root of the tree, which we named R0a3. This new haplogroup shares the T insertion in position 60 and substitution at position 15674 with R0a2, but it does not have the substitution at 2355 and has an additional substitution at 15466.

TMRCA Estimates

The complete sequencing of this large set of R0a samples allowed us to apply both mutation rate estimates recently proposed by Soares et al. (2009), one rate for all positions and one for synonymous substitutions (table 1). The TMRCA obtained with only synonymous substitutions are ∼0.69–1.06 of the dates obtained when analyzing all positions. The relationship between the two TMRCA estimates (mean of 0.854) is not as close as that reported by Soares et al. (2009) (0.9452), demonstrating the randomness inherent in the emergence of neutral mutations as proposed by those authors as the most plausible explanation for differences in TMRCA estimates. For simplicity, in the following description, we refer only to the estimates obtained using all positions.

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Table 1.

Age Estimates and Standard Deviations (in years) for the TMRCA of R0a Haplogroups.

Overall, TMRCA estimates based on all positions, placed R0a and R0a1 in the time frame of 20,000–25,000 YBP (years before present) (22,588 ± 851 for R0a and 21,573 ± 1,325 for R0a1), ages somewhat older than the ones obtained by Abu-Amero et al. (2007), even if those estimates had large confidence intervals, that is, 18,959 ± 8,478 YBP and 18,993 ± 6,999 YBP for R0a (coding region and HVS-1, respectively) and 9,248 ± 7,604 YBP for R0a1 (coding region). Considerable population expansion seems to have occurred ∼12,000–16,000 YBP, with the emergence of the frequent and widespread haplogroups R0a1a (11,489 ± 993 YBP) and R0a2 (15,608 ± 933 YBP) as well as the less frequent and newly identified R0a3 (12,455 ± 3,327 YBP). Other R0a haplogroups seem to have emerged in the period between 5,000 and 11,000 YBP, with some being restricted to the Arabian Peninsula (such as R0a2c and an R0a1a haplogroup defined by 3438-5120-5333 both haplogroups have TMRCA estimates of 8,784 ± 2,744 YBP), whereas other haplogroups were observed in North and East Africa (R0a2a—6,549 ± 2,045 YBP; R0a2b—10,063 ± 2,298 YBP; and an R0a2 haplogroup defined by a substitution at position 9128—6,094 ± 2,268 YBP). The two branches restricted to Soqotra and neighboring regions in Yemen display TMRCAs of 3,160 ± 943 YBP (R0a1a1a) and 3,030 ± 1,120 YBP (R0a2f1 plus a substitution at position 11365), overlapping but narrowing the estimates previously reported when based only on HVS-1 variants (3,363 ± 2,378 YBP; Černý et al. 2009). Curiously, both R0a1a1a and R0a2f1 branches share the highly recurrent substitution at position 13708, which is a replacement substitution on the protein-coding gene ND5, converting an alanine (neutral apolar) to a threonine (neutral polar) (Pereira et al. 2009; Soares et al. 2009).

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Discussion

In this work, we provide genetic evidence in support of human demographic expansions in South Arabia during the last 20 KYA when the climate was rapidly improving. We show that there is a statistically significant clustering pattern of mitochondrial haplogroups R0a throughout the Arabian Peninsula, reaching its highest frequency (∼30%) in southeast Yemen and especially on Yemen’s Soqotra Island. The distribution of Moran’s I index versus distance classes suggests a clinal distribution of R0a and R0a1a (fig. 1), although there are some nonsignificant values likely reflecting the heterogeneity of Arabia’s natural landscape where inhospitable desert alternates with more habitable oases and mountains. Furthermore, heterogeneity of sampling may play a role; in fact, when assaying fewer samples inside Yemen, the cline was clearer with four out of five points showing statistical significance (data not shown). Unfortunately, no available data from Oman were available to us.

Current evidence favors the introduction of R0 to Arabia from the Middle East, where the oldest lineages for the R clade are observed (Richards et al. 2000). However, it is possible that Arabia was an additional centre for R0 emergence. Our results show that several founders of R0a are present in southern Arabia, with TMRCA estimates suggesting population continuity between the terminal Pleistocene and Holocene. Some of these mtDNA lineages also spread to North and East Africa. Two periods of demographic expansions closely match two wet climatic periods: the end of the 35–20 KYA wet period and the brief wet phase between 15 and 13 KYA. The post-LGM expansion around 16 KYA seems to have been especially important (including the new R0a3 haplogroup and the very frequent haplogroup R0a1a with its many branches deriving directly from the root), which is concordant with the hypothesis of human resettlement of Arabia (Parker 2009).

Recent archaeological findings agree with the genetic evidence suggesting population continuity, especially in the Yemeni highlands where two Early Holocene pre-Neolithic and Neolithic sites have been identified (Fedele 2009). However, there also exists the hypothesis that the peopling of eastern Arabia by Pre-Pottery Neolithic B-related settlers was the result of widespread population dispersal during the Early Holocene (Uerpmann et al. 2009). Fedele (2009) examined this issue in the Yemeni highlands, where archaeological surveys at two sites attested to an Early Holocene “Pre-Neolithic” settlement throughout the eastern Yemen Plateau (and a single continuum from Pre-Neolithic to Neolithic) with features of its Pre-Neolithic industry displaying hints of similarity with East Africa rather than the Fertile Crescent. Further study (McCorriston and Martin 2009) focused on the Early Holocene pastoralists along the desert margins of southern Arabia and found evidence for cattle introduction from the Levant or possibly from northeastern Africa by the sixth millennium BC, if not earlier. They suggest multiple waves of expansion into Arabia, at different times, and even suggest that the earliest herd animals in southern Arabia were probably introduced as a pioneering strategy among local hunters.

Our results show that a substantial part of the Yemeni population is biologically related to one or more demographic expansion events that have taken place over the last 20 KYA. The southeast parts of Yemen, such as Al Mahra Hadramawt and mainly Soqotra might have played an important role in later demographic expansion, as R0a1a1a and R0a2f1 now testify. The place where these haplogroups were identified closely match a South Arabian refugium suggested by paleoclimatic data (Rose and Petraglia 2009) and show the importance of the Holocene in this area. It would be very informative to have R0a sequences from Oman (especially Dhofar) in order to more precisely localize the origin of these genetically apparent demographic upheavals. It is very interesting that the genetic dates for the introduction and expansion of Soqotran R0a clades (between 6 and 3 KYA) match the earliest evidence for seafaring activity in the peninsula in the sixth millennium BC (Boivin et al. 2009). Our study is thus an example of how results in human genetics can closely overlap with other fields of anthropology.

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Supplementary Material

Supplementary materials 1–3 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).

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Acknowledgments

This project was supported by the Fulbright-Masaryk Fellowship of V.C. at the Department of Anthropology, University of Florida, the Ministry of Education of the Czech Republic, Grant number: KONTAKT ME 917, the Council of American Overseas Research Centers, the American Institute for Yemeni Studies, and the Portuguese Fundação para a Ciência e a Tecnologia (PTDC/ANT/66275/2006) (L.P.), (Instituto de Patologia e Imunologia Molecular da Universidade do Porto is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by the Portuguese Foundation for Science and Technology, FCT). This research was also supported by a grant from the National Science Foundation to C.J.M. (BSR-0518530).

Haplogroup R (mtDNA)

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Haplogroup R
Possible time of origin	66,000 YBP ^[1]
Possible place of origin	South Asia
Ancestor	N
Descendants	R0, R1, R2'JT, R3, R5, R6'7, R8, R9, R11'B, R12'21, R14, R22, R23, R30, R31, P, U
Defining mutations	12705, 16223^[2]

In human mitochondrial genetics, haplogroup R is a very extended mitochondrial DNA (mtDNA) haplogroup and is the most common macro-haplogroup in West Eurasia.

Haplogroup R is a descendant of macro-haplogroup N. Among its descendant haplogroups are B, U (and thus K), F, R0 (and thus HV, H, and V), and the ancestral haplogroup of J and T.

Origin

As of June 2009, the most recent study dates the origin of haplogroup R to 66.6kya with a 95% confidence interval of 52.6-81kya.^[1]^[3]

South Asia lies on the way of earliest dispersals from Africa and is therefore a valuable well of knowledge on early human migration.^[4] The analysis of the indigenous haplogroup R lineages in India points to a common first spread of the root haplotypes of M, N, and R along the southern route some 60–70 kya.^[5]

Haplogroup R has wide diversity and antiquity among varied ethnic status and different language families in South Asia. In Indian western region among the castes and southern region among the tribes show higher haplogroup diversity than the other regions, possibly suggesting their autochthonous status.^[6]

Distribution

R and its descendants are spread all over Eurasia, Oceania and the Americas. These descendants are specially prevailing in Western Eurasia. About 89% of Europeans are of mtDNA macro-haplogroup R.^[7]

Subclades

Haplogroup R
- R0 or pre-HV
  - R0a or (preHV)1: Higher frequencies occur in Southwest Asia, specially in the Arabian Plate.^[8] Smaller frequencies in North Africa, the Horn of Africa, South Asia & Europe.
  - HV: It is a west Eurasian haplogroup mainly found throughout the Middle East, including Iran.^[9] It is also found in North Africa, Central Asia and South Asia.
    - HV0 or Pre*V: Mainly in Western Europe.^[10]
      - V: Found at moderately low frequencies around Europe; the highest frequency is in the Sami people 40%.^[11]
    - HV1: Mainly in the Middle East.^[8]
    - HV2: Mainly in South Asia.^[9]
    - HV3: Mainly in Eastern Europe.^[12]
    - H: In West Eurasia. It is the most common mtDNA haplogroup in Europe.
- R1
  - R1* (16278): In Kurdish from Turkmenistan (9%).^[9]
  - R1a
    - R1a* (3337): Found in Brahmins from Uttar Pradesh (India).^[5] Also in Adygei people (Caucasus).
    - R1a1: Found in Northwest Caucasian people like Kabardins and Adygei people. Observed in eastern European populations like northwestern Russians and Poles.^[12]
- pre-JT or R2'JT
  - R2: Found mainly in Balochistan (Pakistan).^[9]
    - (13500): Found in Rajasthan and Uttar Pradesh (India).^[4]
    - (150, 303+1C): In Iran, Georgia and Turkey.
  - JT
    - J: The highest frequency is in the Near East (12%), 21% in Saudi Arabia.^[8] J declines towards Europe at 11%, Caucasus 8%, North Africa 6% and becomes practically missing in East Asia.^[13]
    - T: The highest frequency is in the Caspian region (Caucasus, Northern Iran, Turkmenistan).^[9] It is important in Europe (almost 10%),^[14] Middle East, Central Asia, Pakistan and North Africa. Small frequency in the Horn of Africa and India.
- R3: Found in Armenia.^[15]
- R5: Widely spread in the Indian subcontinent. Specially in Madhya Pradesh (India) at 17%.^[16]
  - R5a
    - R5a1: Found within the Indo-European speaking populations of India.^[17]
    - R5a2: Specially among Dravidic groups of India and Sri Lanka.^[17]
- R6'7 (16362) The most important presence is among Austroasiatic language-speakers from India (10%).^[17]
  - R6: Small frequencies in India and Pakistan.^[16]
  - R7: In the Indian subcontinent (see map).^[17]
    - R7a: Mainly in East India, specially in Santals from Bihar and Jharkhand. (map)
    - R7b: Specially in Dravidian tribes of East India. (map)
- R8: The highest frequency occurs towards East India, especially within Orissa (12%), and it is found among the Austroasiatic tribes (Munda speakers). It is also present in low frequency among the Dravidian and Indo-European speaking family (see map).^[18]
  - R8a: Found mainly in Orissa and Andhra Pradesh (India).
  - R8b: In Orissa, Gujarat, Andhra Pradesh (India).
- R9 (16304)
  - R9b: It appears mostly in Southeast Asia.^[19] Found all over Indonesia, in Indochina, Malaysia, in Aboriginal Malays like Semelai at 28% and Temuan 21%.^[20]
  - (249d)
    - R9c: All over the Malay Archipelago and Taiwan. Mainly in Batak (Palawan) at 58% ^[21] and Alor (Indonesia) at 11%.^[22]
    - F: Fairly common in East Asia and Southeast Asia. Higher frequencies occur in some areas like Nicobar at 50% and Arunachal Pradesh 31% (India),^[16] and Shors people from Siberia at 44%.^[23] There is also an important frequency in Taiwanese aborigines, Guangdong (China), Maluku (Indonesia), Thailand and Vietnam.
- R11'B (16189)
  - R11: Found in China, mainly in Lahu people from Yunnan at 12.5%.^[24] Also in Japan and Rajasthan (India).
  - B
    - B4: It is found often in East Asia, Southeast Asia, Polynesia, Melanesia, Micronesia, Madagascar and Indigenous peoples of the Americas.
    - B5: Spread in East Asia and Southeast Asia.
  - R24: Found in Philippines.^[25]
- R12'21
  - R12: Found in Australia.^[26]
  - R21: In indigenous peoples of Malaysia like Jahai Negritos at 63%^[20] and Senoi 37%.
- R14: Found in Papua New Guinea,^[27] Nicobar Islands^[6] and Lesser Sunda Islands.^[28] Also known as R12.
- R22 or R12: Typical for Eastern Indonesia, specially in Lesser Sunda Islands (8%).^[22] Low in Thailand.
- R23: Small clade found in Bali and Sumba (Indonesia).^[22]
- R30
  - R30a: Found in Andhra Pradesh, Uttar Pradesh (India), in the Tharu people from Nepal^[29] and Sinhalese people from Sri Lanka.^[17]
  - R30b: Found in Punjab.^[17]
  - R30* (1598, 16189): Found in Punjab, Nepal and Japan.^[29]
- R31
  - R31a: In Brahmins from Uttar Pradesh^[5] and Rajputs from Rajasthan (India).^[17]
  - R31b: In Reddys from Andhra Pradesh (India).^[5]
- P: It is characteristic of Sahul. Found in Philippines and East Indonesia.
  - (16176)
    - P1: Widespread in Melanesia. Higher frequencies occur in Papua New Guinea.^[30] Also found in Maluku, Nusa Tenggara and Polynesia.^[31]
    - P2'10
      - P2: In Melanesia,^[30] specially in New Guinea and New Caledonia.
      - P10: Found in Philippines.^[25]
    - P9 (or AuE): In Aboriginal Australians from the central region.^[32]
  - P3: In Australia and Melanesia.^[30]
  - P4: In Australia and Melanesia.^[33]
- U
  - U1: It appears mostly in the Middle East and Caucasus. Found from India to the Mediterranean and to the rest of Europe.^[34]
  - U5: Approximately 11% of total Europeans and 10% of European-Americans. The highest frequency is in the Sami people.^[11]
  - U6: It is common in North Africa (around 10% of the people) ^[35] with a maximum of 29% in Algerian Berbers^[36]
  - U2'3'4'7'8'9 (1811): Widely spread in West Eurasia and the Indian subcontinent.
    - U8
      - K

Tree

This phylogenetic tree of haplogroup R subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation^[2] and subsequent published research.

R
- R0 (formerly pre-HV)
  - R0a
    - R0a1
    - R0a2
  - HV
    - HV0 (formerly pre-V)
      - HV0a
        V
    - H
- R1
  - R1a
    - R1a1
      - R1a1a
- R2'JT
  - R2
  - JT
    - J
    - T
- R5
  - R5a
    - R5a1
      - R5a1a
    - R5a2
      - R5a2a
      - R5a2b
        R5a2b1
        R5a2b2
        R5a2b3
        R5a2b4
- R6'7
  - R6
    - R6a
      - R6a1
        R6a1a
  - R7
    - R7a
      - R7a1
        R7a1a
        R7a1b
        R7a1b1
        R7a1b2
    - R7b
      - R7b1
        R7b1a
- R8
  - R8a
    - R8a1
      - R8a1a
        R8a1a1
        R8a1a2
        R8a1a3
      - R8a1b
    - R8a2
  - R8b
    - R8b1
    - R8b2
- (16304)
  - R9
    - R9b
      - R9b1
      - R9b2
    - R9c
    - F
    - R22
- R11'B (16189)
  - R11
    - R11a
  - B
  - R24
- R12'21
  - R12
  - R21
- R14
- R23
- R30
  - R30a
  - R30b
    - R30b1
- R31
  - R31a
    - R31a1
  - R31b
- P
- U

Princess Maria's DNA results

Princess Maria Sviatopolk-Mirski took a mitochondrial DNA test with Family Tree DNA at this year's Who do you think you are? Live show in London. We now have her DNA results which have been very interesting and a big surprise. We inherit mitchochondrial DNA (mtDNA) from our mothers, and an mtDNA test therefore tells us about our direct maternal line - our mother, our mother's mother, our mother's mother's mother and so on back in time for hundreds and thousands of years.

Princess Maria's maternal line can currently be traced back for three generations to her great-grandmother. Princess Maria's mother, Princess Nadezhda Ivanovna Sviatopolk-Mirskaya, was born on 5th July 1903 in Zhitomir, Ukraine. She was the daughter of Prince Ivan Nicolaevitch Sviatopolk-Mirski (1872-1922) and Nadezhda Vassilievna Engelhardt (1879-1954). The Sviatopolk-Mirskis are a family of Polish and Russian nobility with roots in Belarus.

Their ancestral home, Mir Castle in Mir, Belarus, was purchased by Princess Maria's great-grandfather, Prince Nicolai Ivanovitch Sviatopolk-Mirski, in 1895 and remained in the family until 1939. During World War II it was under the control of the Nazis, serving as a ghetto for the local Jewish population prior to their liquidation. It is now a World Heritage Site and is being restored by UNESCO. Princess Maria has been back to Belarus several times in recent years to visit her ancestral home, and is planning another visit this summer. The picture belows shows Princess Maria outside the Sviatopolk-Mirski family chapel at Mir Castle.

The next photo shows Princess Maria's mother Princess Nadezhda as a young girl at Mir Castle.

Princess Nadezhda married her first cousin Prince Semeon Semeonovitch Sviatopolk-Mirsky (1910-1989), the son of Prince Semeon Nicolaevitch Sviatopolk-Mirsky (1885-1917), in about 1931. The wedding took place at Mir Castle. Their first two children were born at Mir Castle: Sebastian in 1933, and Anastasia in 1935. For reasons which are not yet known they were forced to leave the castle and spent the next decade or so living in different European countries. Their third child, Irene, was born in Poland in 1937. Sadly their son Sebastian died in Bydgoszcz, Poland, in 1942. They also lived for a time in Hungary before moving to Germany where Princess Maria was born in 1946 in Meiningen. The photograph below shows Princess Maria's brother Sebastian with her sisters Irene (left) and Anastasia.

In February 1948 Princess Maria's family moved to England, settling briefly in Earls Court in London before moving to Wales in 1949. Princess Maria's father Simeon had served in the Polish army but after arriving in the UK had to work as a painter and decorator.

Her mother had to abandon her dreams of becoming a professional painter and instead worked in cafes, preparing sandwiches, and in hospitals as a ward orderly. Semeon and Nadezhda divorced in the 1950s. Nadezhda then married John Stepanovitch Ilchenko. She died on 21st January 1983 at the Royal London Hospital in Whitechapel at the age of 79.

Princess Maria's maternal grandmother, Nadezhda Vassilievna Engelhardt, was born on 21st March 1879 in Stupina, Smolensk, Russia, the daughter of Nadezhda Nikolaevna Tchapline. She married Prince Ivan Nicolaevitch Sviatopolk-Mirski (1872-1922), a cavalry officer in the Russian Imperial Army, on 27 April 1898 at Novocherkassk, Caucasus, Russia. The photo below is of Prince Ivan and Princess Nadezhda Sviatopolk-Mirski.

Prince Ivan died on 10th February 1922 at Mir Castle. Nadezhda then married Pavel Kondratenko and went to live in Argentina. She died on 12th June 1954 at the age of 75 in Buenos Aires.

We currently know nothing about Princess Maria's maternal great-grandmother, Nadezhda Nikolaevna Tchapline, other than the fact that she was born in 1859, presumably in Russia. She married into the Engelhardt family, a well-known Russian family from Smolensk, but the name of her husband is not yet known. Anastasia Vladimirovna Tikhonova, an historian and a lecturer at Smolensk State University, has been working on the genealogy of the Engelhardt family for many years and is sending Princess Maria further details on the Engelhardts.

We now turn to Princess Maria's DNA results. An mtDNA test can be used for genealogical purposes but will also tell us about our deep maternal ancestry through our haplogroup designation. Even though our paper trail might only go back for a couple of hundred years at most, the mitochondrial DNA we inherit from our mothers has barely changed in thousands of years and therefore provides a unique window into the past.

There are only tiny differences in the mitochondrial DNA of all humans, but these small differences can be used to divide us into different clans or branches of the human family tree which are known as haplogroups. All the branches eventually converge in Africa. We all descend from one woman, known as mitochondrial Eve, who lived in Africa probably around 150,000 years ago. She is not the first human female to live on the planet but is simply the only woman whose daughters and female descendants have survived through to the present day. The mtDNA haplogroups often correlate with specific geographical areas. Haplogroups A, B, C, D and X are, for instance, found in native Americans. Haplogroups L1, L2 and L3 are usually only found in Africa. In Europe the principal haplogroups are H, I J, K, T, U, V, W and X. This page on the Eupedia website shows how all the European mtDNA haplogroups fit together.

Princess Maria's DNA results however show that she is not in any of the major European haplogroups and instead belongs to the very rare and ancient haplogroup known as ROa, a small branch of haplogroup RO, which was previously known as haplogroup pre-HV. Spencer Wells, in his book Deep Ancestry: Inside the Genographic Project, tells us that:

Individuals in haplogroup pre-HV can be found all around the Red Sea and widely throughout the Near East. While this genetic lineage is common in Ethiopia and Somalia, individuals from this group are found at highest frequency in Arabia. Because of their close genetic and geographic proximity to other western Eurasian clusters, members of this group living in eastern Africa are the likely result of more recent migrations back in to the continent.

Haplogroup pre-HV descends from R and is sometimes referred to as RO. These descendants live in high frequencies in the Anatolian/Caucasus region and Iran. While members of this group can also be found in the Indus Valley near the Pakistan-India border, their presence is considered the result of a subsequent migration eastwards of individuals out of the Near East...

Other members of pre-HV moved north across the Caucasus Mountains and west across Anatolia, their lineages being carried into Europe for the first time by the Cro-Magnon.

Very little seems to be known about haplogroup ROa, Princess Maria's branch of RO. It is found primarily in Europe but only at very low frequencies. It is possibly one of the original mitochondrial haplogroups in Europe, pre-dating the spread of agriculture around 10,000 years ago. There are very few samples of ROa in any of the databases, and Princess Maria is quite possibly the first or one of the first few people living in the UK to be tested with this haplogroup.

Family Tree DNA have haplogroup projects for all the mtDNA haplogroups. Princess Maria has now joined the haplogroup R project at FTDNA which encompasses haplogroup R and all the R subclades. As can be seen from the project results page here she is one of just 13 people in the project belonging to haplogroup ROa.

Princess Maria's DNA results have also been uploaded to Mitosearch, the public mtDNA database which is used by mtDNA researchers. Her results can be found on Mitosearch here. At the time of writing Princess Maria is just one of 41 people in the Mitosearch database belonging to haplogroup ROa as can be see here.

Family Tree DNA have a huge mtDNA database with almost 110,000 samples from all over the world. Not everyone who has taken an mtDNA test will necessarily join a haplogroup project or upload their results to Mitosearch. I therefore asked Eileen Krause Murphy, the mtDNA specialist at Family Tree DNA, if she could provide me with some statistics on mtDNA haplogroup ROa and its distribution. She kindly replied as follows and her comments are published here with her permission:

We have about 350 ROa's in our database. I looked up the geographic frequencies for the ones who reported a country of origin.

Greater than 10% of ROa's:
Ethiopia 13%

5-10%: (from most frequent to least)
Italy
Yemen
Russia
Israel
Poland
Germany
Lithuania

1-5%: (from most frequent to least)
Ukraine
Lebanon
Belarus
Greece
Libya
Romania
Saudi Arabia
Tunisia
France
Hungary
Netherlands
Portugal
Turkey

Please note these frequencies are slightly biased by the inclusion of research study data which focused on certain populations. Still, this is perhaps helpful in identifying the geographic spread of ROa. I included those who have upgraded to the full sequence and belong to one of the branches of ROa.

There is clearly still a lot more to be learnt about the origins and the migratory path of haplogroup ROa and the picture will no doubt become clearer as more people take mtDNA tests and more ROa samples are added to the databases. Princess Maria was very excited to belong to such a rare and interesting haplogroup.

From the genealogical point of view we hope to find matches within the mtDNA databases with our genetic cousins. Our closest genetic mtDNA cousins are those people who belong in the same haplogroup as us. Within our personal haplogroup we are most closely related to those people who have identical mtDNA results. The more mismatches the more distant the shared common ancestor. With the more common haplogroups, such as haplogroup H, people can often have literally thousands of matches at the basic HVR1 level, which is effectively a low-resolution test.

With the addition of HVR2 the matches are refined but people can still often have lots of matches. In contrast, Princess Maria does not currently have any matches, even at the HVR1 level. An mtDNA test is however an excellent investment because your test continues to work for you by staying in the databases and as more people get tested I would hope that Princess Maria will eventually have some matches which will provide further clues to her maternal Russian ancestry.

Maternal Haplogroup R

martes, 12 de febrero de 2013

Haplogroup R0 (mtDNA)

From Wikipedia, the free encyclopedia

Contents

Origin

Distribution

Subclades

Tree

See also

References

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Internal Diversification of Mitochondrial Haplogroup R0a Reveals Post-Last Glacial Maximum Demographic Expansions in South Arabia

Abstract

Key words

Introduction

Materials and Methods

Samples

Laboratory Work

Phylogenetic Analyses

Interpolation Maps and Evaluation of Spatial Autocorrelation

Results

Frequencies and Geographic Distribution of R0a Haplogroups

R0a Phylogenetic Tree Based on Whole-Genome Information

TMRCA Estimates

Discussion

Supplementary Material

Acknowledgments

Haplogroup R (mtDNA)

Contents

Origin

Distribution

Subclades

Tree

Princess Maria's DNA results

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