The modern distribution of R1a1 has two widely separated areas of high frequency, one in South Asia, around India, and the other in Eastern Europe, around Poland and Ukraine. The demographic reasons for this are the subject of on-going discussion and attention among population geneticists and genetic genealogists.
Until 2012, there was extensive scholarly debate as to the origins of haplogroup R1a1. Some researchers found that Indian, or more generally, South Asian populations, had the highest STR diversity. Other studies variously proposed Eastern European, Central Asian and even Western Asian origins for the R1a1.
Archaeologists recognize a complex of inter-related and relatively mobile cultures living on the Eurasian steppe, part of which protrudes into Europe as far west as Ukraine. These cultures from the late Neolithic and into the Iron Age, with specific traits such as Kurgan burials and horse domestication, have been associated with the dispersal of Indo-European languages across Eurasia. Nearly all samples from Bronze and Iron Age graves in the Krasnoyarsk area in south Siberia belonged to R1a1 and appeared to represent an eastward migration from Europe. In central Europe, Corded Ware period human remains at Eulau from which Y-DNA was extracted appear to be R-M17(xM458) (which they found most similar to the modern German R-M17* haplotype.
Besides these, studies show high percentages in regionally diverse groups such as Manipuris (50%)(Underhill 2009) to the extreme North East and in Punjab (47%)(Kivisild 2003) to the extreme North West.
Wells 2001, noted that in the western part of the country, Iranians show low R1a1 levels, while males of eastern parts of Iran carried up to 35% R1a1. Nasidze 2004 found R1a1 in approximately 20% of Iranian males from the cities of Tehran and Isfahan. Regueiro 2006 in a study of Iran, noted much higher frequencies in the south than the north.
Further to the north of these Middle Eastern regions on the other hand, R1a1 levels start to increase in the Caucasus, once again in an uneven way. Several populations studied have shown no sign of R1a1, while highest levels so far discovered in the region appears to belong to speakers of the Karachay-Balkar language among whom about one quarter of men tested so far are in haplogroup R1a1 (Underhill 2009).
Haplogroup R1a1 was found at elevated levels among a sample of the Israeli population who self-designated themselves as Levites and Ashkenazi Jews (Levites comprise approximately 4% of Jews). Behar reported R1a1 to be the dominant haplogroup in Ashkenazi Levites (52%), although rare in Ashkenazi Cohanim (1.3%). (Behar 2003).
The remains of a father and his two sons, from an archaeological site discovered in 2005 near Eulau (in Saxony-Anhalt, Germany) and dated to about 2600 BCE, tested positive for the Y-SNP marker SRY10831.2. The Ysearch number for the Eulau remains is 2C46S. The ancestral clade was thus present in Europe at least 4600 years ago, in association with one site of the widespread Corded Ware culture (Haak 2008).
R-M458 This branch is found almost entirely in Europe, and with low frequency in Turkey and parts of the Caucasus. Its highest frequencies were found in Central and Southern Poland, particularly near the river valleys flowing northwards to the Baltic sea (Underhill 2009).
R-M334 is defined by the M334 marker. However this mutation was found only in one Estonian man and may define a very recently founded and small clade (Underhill 2009).
R-M458 is a mainly Slavic SNP, characterized by its own mutation, and was first called cluster N. Underhill et al. (2009) found it to be present in modern European populations roughly between the Rhine catchment and the Ural Mountains and traced it to "a founder effect that [...] falls into the early Holocene period, 7.9±2.6 KYA." M458 was found in one skeleton from a 14th-century grave field in Usedom, Mecklenburg-Vorpommern, Germany. The paper by Underhill et al. (2009) also reports a surprisingly high frequency of M458 in some Northern Caucasian populations (for example 27.5% among Karachays and 23.5% among Balkars, 7.8% among Karanogays and 3.4% among Abazas).
The R-L260 lineage, commonly referred to as West Slavic or Polish, is a subclade of the larger parent group R-M458, and was first identified as an STR cluster by Pawlowski 2002 and then by Gwozdz 2009. Thus, R-L260 was what Gwozdz 2009 called cluster "P." In 2010 it was verified to be a haplogroup identified by its own mutation (SNP). It apparently accounts for about 8% of Polish men, making it the most common subclade in Poland. Outside of Poland it is less common (Pawlowski 2002). In addition to Poland, it is mainly found in the Czech Republic and Slovakia, and is considered "clearly West Slavic." The founding ancestor of R-L260 is estimated to have lived between 2000 and 3000 years ago, i.e. during the Iron Age, with significant population expansion less than 1,500 years ago (Gwozdz 2009).
Klyosov 2009 notes a potential clade identified by a mutation on the relatively stable STR marker DYS388 (to an unusual repeat value of 10, instead of the more common 12), noting that this "is observed in northern and western Europe, mainly in England, Ireland, Norway, and to a much lesser degree in Sweden, Denmark, Netherlands and Germany. In areas further east and south that mutation is practically absent."
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