Phase 2: 37 STR analysis Ysearch R1b haplogroup

In an attempt to examine the R1b subclades in greater depth FTDNA 37 marker haplotypes were extracted and edited from Ysearch on 21 June 2005. The individuals had to be classified as R1b or R1a (and subtypes) in the database and whose origin was listed as from Britain, Ireland, Western Europe and Scandinavia. The edited data set contained 713 individuals that had 37 STR genotype scores. Names were concatenated with their Ysearch listed haplogroup and their unique ID to ease future comparison (e.g. Courtney_R1b_E3HBX). In some cases the names were edited or truncated.

The data was clustered using Populations, with Nei’s standard genetic distance and neighbor joining options selected. The resultant data was then displayed as a phylogram and an R1a classified sample NJ9C5 selected as the outgroup. The link to the phylogram is shown below. It is a pdf file so you will need a pdf viewer. Note you can search within the pdf viewer for a surname or unique ID within the phylogram.

37 STR phylogram for Ysearch R1b and R1a classified Irish, British, European and Scandinavian individuals

Based on the cluster order displayed in the phylogram potential R1b subclades were identified visually and statistics calculated on the selected individuals within the subclade. Where possible subgroups identified in the previous 25 STR marker analysis were labeled the same.

Results and discussion

The exact number was not determined, but perhaps one third of the same individuals are as in the previous 25 STR analysis. The R1a classified haplogroup individuals were clustered with no incorrect assignments. The major observation is that the R1b sub-clusters tend to be similar, but with additional sub-clusters defined, and the number of marker differences between sub-clusters has increased. Modal STR haplotypes for tentative R1b sub-clades are shown below.

The process again identified an R1b subgroup labeled R1ba, with 10 differences, which has been previously described by David Wilson http://home.earthlink.net/~wilsondna/DYS392=14%20Summary.htm. This is commonly known as an “Irish R1b variety” even though it is only at a higher frequency in that Island. David Wilson’s modal haplotype R1bdw differs at several markers from this analysis presumably due to sampling.

The next group labeled R1bi with 5 differences. This putative subgroup of R1b identified in the 25 STR analysis was primarily expressed in Britonic surnames and could be called a Campbell/Strathclyde signature. This group is now dubbed “Scot R1b variety” after Ken Nordtvelt who first described it R1bKN and has done an extensive analysis on this grouping, see http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2005-07/1120443313 .

Perhaps surprisingly, three additional subclades have been tentatively identified R1bcc, R1bff, R1bgg with 4, 7 and 6 differences respectively. All have 23 repeats at DYS 390.

Table 2. Modal haplotypes of subclades from Ysearch 37 STR analysis. Old 25 STR subclades are also indicated. R1b* are intermediate haplotypes between R1a and R1b haplogroups that have all been assigned R1b. Only subclades that appear visually distinctive have been annotated on the phylogram, typically those with 5 or more differences.

37 STR	25 STR	n	393	390	19	391	385a	385b	426	388	439	389i	392	389ii*	458	459a	459b	455	454	447	437	448	449	464a	464b	464c	464d	460	H4	YCAIIa	YCAiib	456	607	576	570	CDYa	CDYb	442	438	dif
R1a	R1a	104	13	25	15	11	11	14	12	12	10	13	11	17	15	9	10	11	11	23	14	20	32	12	15	15	16	11	11	19	23	16	16	17	18	34	39	12	11	19
R1b*		24	13	24	14	11	11	14	12	12	12	13	13	17	18	9	10	11	11	25	15	19	29	15	15	16	17	11	11	19	23	16	15	19	17	36	38	12	12	5
R1baa	R1ba	54	13	25	14	11	11	13	12	12	12	13	14	16	17	9	10	11	11	25	15	18	30	15	16	16	17	11	11	19	23	17	16	18	17	37	40	12	12	10
R1bbb		17	13	24	14	11	11	14	12	12	12	13	13	16	18	9	10	11	11	25	15	19	29	15	15	17	17	11	11	19	23	15	15	17	17	37	38	12	12	3
R1bcc		61	13	23	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	29	15	15	17	18	11	11	19	23	17	15	17	17	37	38	12	12	4
R1bdd		48	13	24	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	29	14	15	16	17	11	11	19	23	16	15	18	17	37	37	12	12	3
R1bee		51	13	24	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	29	15	16	17	17	11	11	19	23	16	15	18	17	36	39	12	12	2
R1bff		24	13	23	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	30	15	15	17	17	11	11	19	23	15	14	16	17	36	39	12	12	7
R1bgg		48	13	23	14	10	11	14	12	12	12	13	13	16	16	9	10	11	11	25	15	19	30	15	15	16	17	11	11	19	23	16	15	18	17	35	38	12	12	6
R1bhh		32	13	24	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	30	15	15	16	17	11	11	19	23	16	15	19	17	36	40	12	12	4
R1ba		55	13	24	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	29	15	15	17	17	10	11	19	23	15	15	18	17	36	37	12	12	4
R1bb		51	13	24	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	29	15	15	17	17	11	11	19	23	15	15	18	17	35	38	12	12	2
R1bc		47	13	24	14	11	11	14	12	12	11	13	13	16	17	9	10	11	11	25	15	19	28	15	15	17	17	11	11	19	23	16	15	18	17	36	38	12	12	3
R1bd		47	13	24	14	11	11	15	12	12	12	13	13	16	17	9	10	11	11	25	15	19	29	15	15	16	17	11	10	19	23	15	15	18	16	36	38	12	12	5
R1be	R1bi	50	13	24	14	10	11	14	12	12	12	13	13	17	17	9	10	11	11	25	15	19	30	15	15	17	17	11	11	19	24	16	15	18	17	37	37	12	12	5
total		713
Subgroups
R1baaa	R1ba_core	47	13	25	14	11	11	13	12	12	12	13	14	16	17	9	10	11	11	25	15	18	30	15	16	16	17	11	11	19	23	17	16	18	17	38	40	12	12	11
R1be1	R1bi_core	34	13	24	14	10	11	14	12	12	12	13	13	17	17	9	10	11	11	25	15	19	30	15	15	17	17	11	12	19	24	15	15	18	17	37	38	12	12
Accepted modal haplotypes (web)
R1b			13	24	14	11	11	14	12	12	12	13	13	16	17	9	10	11	11	25	15	19	29	15	15	17	17	11	11	19	23	16	15	18	17	37	38	12	12
R1bdw			13	25	14	11	11	13	12	12	12	13	13	16	17	9	10	11	11	25	15	18	29	15	15	17	17	11	11	19	23	17	16	18	17	38	39	12	12	7
R1bKN			13	24	14	10	11	14	12	12	12	13	13	17	18	9	10	11	11	25	15	19	30	15	15	17	17	11	12	19	24	15	15	18	17	37	38	12	12	7
R1a			13	25	15	10	11	14	12	12	10	13	11	17	15	9	10	11	11	23	14	20	32	12	15	15	16
I1			13	23	15	10	14	14	11	14	11	12	11	16	15	8	9	11	11	23	16	20	29	12	14	15	16
* note 389ii = FTDNA389ii-389i

A preliminary investigation was undertaken examining the age of several of these subclades. Key details are shown in the table below. The method involved taking the members of the subclade and comparing them against the modal estimates for R1b, R1a and I1 and taking the mean estimate. An essential parameter used in these analyses is the mutation rate. A value of 0.00069 +/-0.0006 has been used, based on the estimate of Zhivotosky et al 2004. Further details on this estimate will be posted on the site at a later date.

It should be emphasized that these estimates are subject to great uncertainty and hence so are any conclusions drawn from them.

The R1ba group appears to have diverged some 6783 years after the R1b SWAMH (95% range 4000-10609 years). This is a substantial range. Examining the diversity within the R1ba subclade suggests the TMRCA of R1ba was 4849 years bp (SD 1510) for this group (using 50% threshold for TMRCA). Two observations can be made, first the diversity within the subclade is relatively small compared to its distance from the R1b haplogroup. It also puts the divergence with SWAMH at over 10,000 years bp. The observed pattern suggests a small introduction of R1ba (perhaps by invasion) into primarily Ireland and this was followed by a rapid expansion of numbers around the 5000 years bp. Alternatively, representatives of a previously rare haplotype, within the existing Irish population, expanded/invaded into a new area and then rapidly expanded in numbers. The evidence to date is inconclusive, but I would speculate that it is the former. This date is broadly coincident with the time where the first evidence of widespread agriculture is recorded.

In contrast the R1bi diverged from the R1b SWAMH 3565 years after this common ancestor (95% range 1739-6348). This divergence is some 3200 years earlier then R1ba and its expansion appears to have been slower as well. Examining the diversity within the R1bi subclade suggests the TMRCA is around 3357 years bp (SD 954) for this group using 50% threshold for TMRCA. Combining these suggests R1bi diverged from SWAMH approximately 6500 years bp. Obviously, this is inconsistent with the estimate above and is a function of the fuzziness of the branching process (and probably my use of statistics). The observed pattern suggests a small introduction around 3400 years bp followed by a slower expansion. Alternatively, representatives of a previously rare haplotype, within the existing Scottish population, more slowly expanded in numbers. The evidence is inconclusive at this point.

Table 2. TMRCA estimates derived from http://www.mymcgee.com/tools/yutility.html for selected modal haplotypes from SWAMH R1b using a mutation rate of 0.00069 and 25 years per generation.

Subclade	TMRCA Estimate
	50%	5%	95%	comment
R1b_DW	4174	2174	7130	David Wilson values
R1b_KN	4174	2174	7130	Ken Nordtvelt values
R1a_given	14000	8609	21478	25 marker
I1_given	24087	15652	35565	25 marker
R1a	12522	8261	18087	37 marker this analysis
R1bcc	2435	1043	4783	unknown group?
R1bff	4174	2174	7130	unknown group?
R1bgg	3565	1739	6348	unknown group?
R1ba	6783	4000	10609	R1b_DW equivalent (small group)
R1bi	3565	1739	6348	R1b_KN equivalent

Summary

A semi-independent and more extensive analysis using 37 instead of 25 Y STR markers from Ysearch has identified several R1b subgroups previously identified by others and in the 25 STR phase 1 analysis. It has also identified several new groups worthy of investigation. The results still need to be reconciled with geographic origin of surnames and stated origin of ancestors. In addition more extensive analysis needs to be undertaken of the timing and pattern of divergence. When both are combined it may be possible to tentatively assign these individuals to a probable oral or written historical origin.