The history of this haplotype is as follows. Note that the numbers that follow are all approximate, and I haven't gone back to the sources to find the error bars. Also, here I present only the lineage that leads to me, a summary of other lineages which populated India can be found in my pages dealing with the history of Bengal. In a similar vein, this description only traces back to at most a 100000 years back, you can find a cursory account of human evolution dealing with the period before that here instead. The data that is not from reading the original papers comes from the summary at the isogg web site.
As the Y chromosome is passed on, small ‘mutations’ or copying errors (given names like M17) occur, dividing all of us into haplogroups (e.g., R1a) who share male ancestry. The deepest split is when the A haplogroup split away around 60000 years back (to within large errors), after which my ancestors (called BT or YxA) accumulated the markers SRY1532.1/SRY10831.1 (a / separates alternate names for the same marker; a .1, .2, etc. marks various times the same locus mutated), M42, M94, M139, M294, and P9.1 after splitting from people carrying the haplogroup B, defining the group CF. The first individuals in whom these mutation occurred fathered all individuals living outside Africa, and is fondly called the Eurasian Adam. All we know so far is he lived sometime between 29000 and 77000 B.C. in Africa, some 2500 generations, give or take a 1000, before me; and his descendants had a wanderlust, possibly nomadically following the animals during a period of moist climate, or possibly driven by a population increase resulting from the favourable climate. Whatever be the reason, we see an increasing sophistication in tools and appearance of art as the generations progressed.
A branch of the population that came out of Africa started moving eastward along the coast, and is marked by P143 that probably arose 31–55 thousand years ago (this group is called ‘C,F’ to be distinguished from the parent CF), whereas the other branch (DE; defined by M1/YAP, M145/P205, M203, P144, P153, P165, P167, and P183, which may have arisen in North East Africa around 50000 years back) took a somewhat northern route east. The descendants of both of these are present today in central and southeast Asia (though India except for Tibet and Andaman—both of which are very high in D—sees almost no DE), and descendants of both these groups have migrated back to Africa at various times. After a wave of emigrants (C; defined by M130/RPS4Y711, M216, P184, P255, and P260) left around 50000 years back to ultimately populate the southern coast of Asia all the way to Australia (and also Central Asia and Americas), the markers P14, M89, M213/P137, M235, P133, P134, P135, P136, P138, P139, P149, P141, P142, P145, P146, P148, P149, P151, P157, P158, P159, P160, P161, P163, P166, and P187 made their appearance and we started being called the haplogroup F. Most non-Africans are actually the descendant of an individual carrying these mutations (about 2500 generations back, possibly 60–80 thousand years ago if it arose in Africa), who lived somewhere in northern Africa or just outside near the middle east. Some of his descendants (G; marked by M201, P257, U2, U3, U6, U7, U12, U17, U20, U21, U27, and U33 that arose around 30000 years ago) lived in the northern part of the middle east, but most went through Iran into either India (H; marked by M69 and M370) or the Steppes of Central Asia (IJK), possibly hunting game like buffalo, antelope, and wooly mammoths. These IJK were marked by L15/M523/S137, L16/M522/S138, and L69.1(=G)/S163.1 that arose around 45000 years back, probably while still in the middle east, because some of his descendants (IJ; marked by M429/P125, P123, P124, P126, P127, P129, P130, S2, and S22 that arose around the same time) migrated to both Europe (I) and Asia (J).
Some 5000 years later, and say 1500 generations back, people living in Southwest Asia, may be Iran, developed the markers M9, P128, P131, P132 and all of us who descended from him are classified as haplogroup K (the descendants of the other haplotype F people are today called F*(xK), and so on for the other cases below). His descendants are popularly called the Eurasian clan, and are a vast majority in Asia, Europe, and the Americas, though some K(xLMNOPST) are also found in Africa.
A further mutation M526 separated the group called MNOPS, whose descendants went to Central Asia, from the middle eastern T (marked by M70, M184/USP9Y+3178, M192, and M272) and the Indian L (marked by M11, M20, M22, M61, M185, and M295). The next major set of markers 92R7, M45, M74/N12, P27.1/P207, P69, P226, P228, P230, P235, P237, P239, P240, P243, P244, P281, P282, P283, P284, and P295 marked us as belonging to haplogroup P; as opposed to the east asian M (marked by P256) and S (marked by M230, P202, P204) or the NO clade (marked by M214, P188, P192, P193, P194, and P195) that porbably arose around Mongolia. These mutations defining P probably arose somewhere in central Asia, may be as far South as the Pamir region, or north as Uzbekistan, Kazakhstan or even Souther Siberia, about 35000 BC, still more than a 1000 generations before us. Their descendants started in these game rich regions north of the Hindukush, but ultimately populated most of Europe and the Americas; even while surviving the ice age that was now upon them.
The appearance of M207/Page37/UTY2, P224/PF6050, P227, P229/PF6019, P232, P280, P285, M734/PF6057/S4/YSC0000201, PF6014/S9, and V45 (FTDNA also has L747, F33, F47, F63, F82, F295, F356, F652, PF5953, PF6063, YSC0000067, YSC0000179, YSC0000232, and YSC0000233 in this set) somewhere in Asia around 27000 years ago then made us into group R (also called R-M207) and distinguished us from Q (marked by M242, whose descendants went through the Altai/Baikal region), and M173/P241/Page29, M306/PF6147/S1, P225, P231, P233/PF6142, P234, P236, P242/PF6113, P245/PF6117, P286/PF6136, and P294/PF6112 (FTDNA adds F93, F211, F378, P238, PF6145, YSC0000182, YSC0000207, YSC0000230, and YSC0000288) around 18500 years back in southwestern Asia made it R1 (also called R-M173) (R2, the other defined haplogroup, is marked by M479—this is the new nomenclature from 2010, the till-recent defining marker M124 along with P249, P267, and L266 now marks R2a—instead). The descendants of these people brought cave paintings to Europe. Reality, of course, could be more complicated than captured by this sketch for it is likely that appreciable diffusion and incorporation of outsiders was taking place in those days, migrations are often back and forth movements, the original ‘urheimat’ might have been depopulated, and any migrating group would be genetically heterogeneous to some extent. See the genebase tutorial for a more detailed writeup by them. The following summary is very vaguely based on a recent paper and the ISOGG page on the R haplogroup, see that page for more up to date information.
A further set of mutations, L145/M449/PF6175, L63/M511/PF6203, L62/M513/PF6200 and L146/M420/PF6229 (FTDNA adds: L122 (conflicts ISOGG), L168, L457, M417 (conflicts ISOGG), M420, M516(conflicts ISOGG), CTS1619, CTS2907, CTS3548, CTS5164, CTS8008, CTS8851, CTS9596, CTS10627, CTS11411, CTS11720, CTS11734, F886, F928, F947, F989, F1050, F1088, F1769, F1808, F2215, F2234, F2684, F2901, F2948, F2957, F3159, F3185, F3194, F3197, F3337, F3364, F3398, F3466, F3551, F3570, F4099, PF6151, PF6159, PF6165, PF6167, PF6169, PF6170, PF6210, PF6211, PF6214, PF6215, PF6216, PF6218, PF7530, PF7540, PF7542) that arose somewhere on the north-south corridor between the Indus Valley and the Eurasian Steppes marks as being R1a (FTDNA calls it R-M417, but that conflicts ISOGG, see later) (M343 is the marker for R1b, P25's for R1b1, though reverted in 2% of this clade, and M269 for R1b1a2—till recently R1b1c); after which Page65.2/PF5234/SRY1532.2!/SRY10831.2! (meaning reverting back to the SRY10831- state it had in the A haplogroup), L122/M448/PF6237 (FTDNA has M448 here, L122 before), M459/PF6235, and L120/M516/PF6236 (FTDNA has M516 before, and no L120) marks us as belonging to group R1a1 (also called R-M459); and I belong to R1a1a (also called R-M17) defined by the markers M17, M198/PF6238, M512/PF6239, L168, M514/PF6240, M515, and L449/PF6223 (FTDNA does not have L449, but has PAGES00007) (earlier one did not distringuish this clade). I also have the markers M417, and Page07 defining R1a1a1. (I, however, do not have the markers M56, M157, M64.2, M87, or PK5 that used to define the subclades R1a1a1a-c,e in the 2010 nomenclature and R1a1a2,3,5 earlier; they are now considered private SNPs). The test for P98 (again private; this used to define R1a1a1d in the 2010 tree, and R1a1a4 earlier) was unsuccessful, and I have not been tested for the SNPs defining the new R1a1a1a (R1a1a1i in the 2011 tree) (L664/CTS7083/S298) or the new R1a1a1b (S224/Z645, S441/Z647) clades (containing the R1a1a1g and R1a1a1h of the 2011 tree and R1a1a6,7 from earlier versions) In an old nomenclature, these subclades of R1a1a1 would have been R1a1a/b/c etc.; and though currently I am classified as R1a1a1, it would have been R1a1a in the old classification. Some of my close STR12 matches are from R1a1a1b2a1 L657/S347 subclade of R1a1a1b2a (Z94/F3105, S340, L342.2/S278.2) of R1a1a1b2 (Z93/F992/S202); but one is probably from R1a1a1b1a3b1, and the 1/12 matches are from both R1a1a1b1 and R1a1a1b2 clades. Since the R1a1a1b1/R1a1a1b2 split is probably 12000 years back, finding STR12 matches in both is probably a case of convergence, or we have misdated the split. A complete list of the results of my test is available here: but referring to the outdated 2010 tree.
The R1a1 group probably arose about 20 thousand years ago around the Hindukush mountains (or in Pakistan), and the depth of R1a1a is about 15–16 thousand years in the Pakistan-West India region. From there it may have spread across Nepal and India and to the north-east, reaching the Caucasus by about 12 thousand years ago. From there it seems to have spread to the Southwest through Turkey to Hungary and Greece, the Southeast to Iran, and northwards through Russia. Italy and Kyrgyzstan may have been the last major expansions into fresh territories probably 5.9 and 5.6 thousand years ago. (The eastern European expansion is of the R1a1a1b1 (recently R1a1a1g and, before that, R1a1a7), which arose in Poland about 11 thousand years back, and started spreading by about 8500 years back.) Meanwhile R1a1a1b2 defined by the Z93 mutation probably arose just outside India about 12 thousand years back, and R1a1a1b2a defined by Z94 near the Indian subcontinent probably more than 6000 years back. The history gets murky at this point: it is also possible that Z93 and Z94 arose as far north as the Sintashta culture; L342.2 defining the R1a1a1b2a1 may have spread further among the Andronovo culture, whereas the L342.2- was confined to the Srubna culture in Turkmenistan. In any case, the Z2123 mutation defining R1a1a1b2a1b and Z2124 mutation defining an as yet unnamed clade arose amongst the L342.2+, and probably spread east, west and south from the Indian northwest by about 4000 years back. In this young chronology, L657 defining the R1a1a1b2a1a probably arose on the eastward migration of Z94 people within India, and Y7 defining R1a1a1b2a1a1 arose amongst them around 500 B.C; the Siberian occurences being 16th century admixtures. Alternatively, these groups could have arisen among the Andronovo culture and moved relatively late to India, and were almost lost elsewhere, except isolated instances in Siberia.
These estimates that try to capture isolated tribal populations as well as the more populous groups also use a slow mutation rate estimate, so they are at the older end. The more common estimates use a faster mutation rate and time the major expansions of these groups and typically yield dates about half as old. For example, as illustrated by the maps made by an user called Igor, the major R1a* descendants are found in Europe, who separated from the other branches at about 9000 years back. The R1a1 can then be timed to about 8000–9000 years, and the R1a1a 7200±800 years. R1a1a1b1, the major European and North Eurasian branch, and R1a1a1b2, the South-Eastern branch (including Kyrgyz and Ashkenazi), would both date to 5500±600. R1a1a1b2a1a is the most represented Indian branch that would be dated to 4200±450 years. The European branch splits into Central European R1a1a1b1a1 (3100±350 years, containing the Western Slavic R1a1a1b1a1a at 2775±400 years), Scandinavian R1a1a1b1a3 (5200±600 years) and the rest R1a1a1b1a2 (5000±600 years).
There is some reason to believe that the R1a were the ancestors of the people who spread the Indoeuropean group of languages into Asia, and possibly the Steppes people that domesticated the horse. Of course, if, as seems likely, the R1a haplotype arose thousands of years before the origin of the Indoeuropean group of languages, it probably was present indigenously in various places including India before the advent of Indoeuropean speaking people. Conversely, this late in human history in such a populated region, the amount of linguistic conversion and cultural adoption is expected to be great enough that the people speaking predominantly Indoeuropean languages could often harbour a mixture of haplogroups, and ‘Indoeuropean migrations’ in various regions could even be predominantly represented by different haplotypes. In fact, recent work published shows that the history of the R1a1 people is probably far more complicated than a simple migration of Indoeuropean people either to or from India.