Michael Cooley's Genetic Genealogy Blog GEN • GEN
20 June 2017

Big Y STRs for Cooley Group CF02

To date, three members of Cooley group CF02 have taken the Big Y test: two descendants of early American immigrant Benjamin Cooley (1614-1684), and a descendant of Nehemiah Cooley (c1685-1759), both born in Tring, Herfordshire. There's an advantage in having two or more descendants of the same person test their Y chromosomes: the matching DNA could only have come from one person — the MRCA (Most Recent Common Ancestor). Matching markers, then, provide a DNA print for the ancestor. This is true for both Short Tandem Repeats (STRs) and Single Nucleotide Polymorphisms (SNPs). There's recent news on both fronts.

We've known for some time that the descendants of Benjamin Cooley have two SNPs, A12022 and A12024, that are not found in other CF02 testers. YFull.com has recently finished their analysis of the Big Y for kit #559256, the descendant of Nehemiah Cooley, uncovering a third mismatched SNP, Y23835. This new discovery has been confirmed by two other non-Benjamin test subjects, both negative for the SNP. The SNP, however, hasn't altered the basic CF02 SNP tree structure. Instead, it has merely added an additional marker to the A12022 SNP block:



In addition to peeking at ten million nucleotide bases, the Big Y extracts up to 500 STRs. Whereas SNPs are single-point mutations, an "A" becoming a "G," for example, STR mutations alter the count of a set of nucleotide bases. In other words, 13 sets (or repeats) of AGAA, might become 12 or even 15 repeats in subsequent generations. Perhaps it's simply because so many more elements are involved in STRs (as opposed to the single base in a SNP mutation) that there's a larger degree of randomness. In any case, STRs tend to be somewhat flaky and maintain consistency only to a point. It stands to reason, then, that the more STRs that are sequenced, the greater the number of discovered mutations. For example, the two Benjamin Big Y testers have only four differences among the 37 STRs tested at FTDNA, but 22 differences (per YFull's count, 29 by my count) among the 500 Big Y STRs.1

But counting the genetic distance (GD) between any two testers isn't really the way to go. For one thing, the comparisons become rather complex when dealing with multiple testers. Instead, a modal haplotype is determined, values that are found to be the most common values among testers in the group. Group members are then compared to that.

For example, among the five testers for marker DYS458 (line 13 in the next table), the value of 19 is most common, and 19 is, therefore, the modal value (pink column) at that position. We can readily see that kit #559256 is a GD of 2 for DYS458.


GO TO BOTTOM OF TABLE

Modal #128108   #319005   #559256   #241202   #511271 
1.DYS393131313131313
2.DYS390232323232323
3.DYS19151515151515
4.DYS391111111111111
5.DYS385.1101010101010
6.DYS385.2151515151515
7.DYS426121212121212
8.DYS388121212121212
9.DYS439121213121212
10.DYS389I131313131313
11.DYS392131313131313
12.DYS389II292929292929
13.DYS458191919171919
14.DYS459.1999999
15.DYS459.210910101010
16.DYS455111111111111
17.DYS454111111111111
18.DYS447262626252626
19.DYS437141414141414
20.DYS448191919191919
21.DYS449292929282929
22.DYS464.1151515151515
23.DYS464.2151515151515
24.DYS464.3171717171717
25.DYS464.4171717171717
26.DYS460111111111111
27.Y-GATA-H4101010101010
28.YCAII.1191919191919
29.YCAII.2222222222222
30.DYS456151515151515
31.DYS607151515151515
32.DYS576191919191919
33.DYS570161616161616
34.CDY.1383836373837
35.CDY.2383840383938
36.DYS442121212121212
37.DYS438121212121212
38.DYS531111111111111
39.DYS578999999
40.DYF395.1151515151515
41.DYF395.2161616161616
42.DYS590888888
43.DYS537101010101010
44.DYS641101010101010
45.DYS472888888
46.DYF406101010101010
47.DYS511101010101010
48.DYS425121212121212
49.DYS413.12322--2323
50.DYS413.22323--2323
51.DYS557161616161616
52.DYS594101010-1010
53.DYS436121212121212
54.DYS490111111111212
55.DYS534161616161616
56.DYS450888-88
57.DYS444121212121212
58.DYS481222222222222
59.DYS520212121212121
60.DYS446131313131313
61.DYS61712---1212
62.DYS568111111-1111
63.DYS48713---1313
64.DYS57211---1111
65.DYS640111111111111
66.DYS492121212121212
67.DYS56512-12-1212
68.DYS710363635363636
69.DYS485151515151515
70.DYS632999999
71.DYS495161616161616
72.DYS54012-12121212
73.DYS714262625272626
74.DYS7162626--2626
75.DYS717191919191919
76.DYS505121212121212
77.DYS556111111111111
78.DYS549121212121212
79.DYS589121212121212
80.DYS522101010101010
81.DYS494999999
82.DYS533121212121212
83.DYS636121212121212
84.DYS575101010101010
85.DYS638111111111111
86.DYS462111111111111
87.DYS452292929292929
88.DYS445121212-1212
89.Y-GATA-A10131313131313
90.DYS46324---2424
91.DYS441131313131313
92.Y-GGAAT-1B07101010101010
93.DYS525101010101010
94.DYS712212121212122
95.DYS593151515151515
96.DYS650202020-2020
97.DYS532131313131413
98.DYS715242424242424
99.DYS504161616161616
100.DYS513121212131212
101.DYS561151515151515
102.DYS552252525252526
103.DYS726121212121212
104.DYS635232323232323
105.DYS587181818181818
106.DYS643101010101010
107.DYS49714-14-1414
108.DYS510171717171717
109.DYS434999999
110.DYS461131313131313
111.DYS435111111111111
112.ATA71D03------
113.DXYS15612-12---
114.DYF371.110101010--
115.DYF371.212121212--
116.DYF371.312121212--
117.DYF371.413131313--
118.DYF380.110101010--
119.DYF380.210101010--
120.DYF381.18888--
121.DYF381.28888--
122.DYF38213--13--
123.DYF383.19999--
124.DYF383.29999--
125.DYF384.17777--
126.DYF384.28888--
127.DYF385.110101010--
128.DYF385.211111111--
129.DYF386.111111111--
130.DYF386.211141111--
131.DYF386.314141414--
132.DYF386.414141414--
133.DYF387.130303030--
134.DYF387.231313131--
135.DYF38911111111--
136.DYF391.19999--
137.DYF391.29999--
138.DYF3928888--
139.DYF39327272725--
140.DYF394------
141.DYF396.18888--
142.DYF396.28888--
143.DYF398.18888--
144.DYF398.217171717--
145.DYF399.123232323--
146.DYF399.224242426--
147.DYF399.3-272628--
148.DYF400.1222222---
149.DYF400.2222222---
150.DYF401.115151515--
151.DYF401.216161615--
152.DYF403.126252626--
153.DYF403.228282828--
154.DYF404.114141414--
155.DYF404.216161616--
156.DYF405.16666--
157.DYF405.211111111--
158.DYF407.112121212--
159.DYF407.212121212--
160.DYF408.18888--
161.DYF408.213131313--
162.DYF409.113131113--
163.DYF409.213131313--
164.DYF410.110101010--
165.DYF410.212111212--
166.DYF411.111111111--
167.DYF411.211111111--
168.DYF412.111111111--
169.DYF412.212121212--
170.DYR117171717--
171.DYR1010101010--
172.DYR10010101010--
173.DYR10110101010--
174.DYR1027-7---
175.DYR1039-9---
176.DYR1049999--
177.DYR1055-5---
178.DYR1068888--
179.DYR107------
180.DYR1089999--
181.DYR1105555--
182.DYR11111111111--
183.DYR11213131313--
184.DYR1136666--
185.DYR114------
186.DYR11529-29---
187.DYR1164444--
188.DYR1177777--
189.DYR11810101010--
190.DYR11911111111--
191.DYR1210101010--
192.DYR1206666--
193.DYR121.114--14--
194.DYR121.214--14--
195.DYR122.17-77--
196.DYR122.27-77--
197.DYR12317171717--
198.DYR124.19999--
199.DYR124.210101010--
200.DYR124.3-111210--
201.DYR125.124242224--
202.DYR125.225252525--
203.DYR12613131313--
204.DYR127------
205.DYR128.19999--
206.DYR128.210101010--
207.DYR1312121212--
208.DYR13013131313--
209.DYR1317777--
210.DYR132.112--12--
211.DYR132.212--12--
212.DYR13511111111--
213.DYR1366666--
214.DYR1374444--
215.DYR13817171717--
216.DYR13918191818--
217.DYR1411101111--
218.DYR14311111111--
219.DYR144999---
220.DYR1469999--
221.DYR1512121212--
222.DYR15013131313--
223.DYR15210101010--
224.DYR15412121212--
225.DYR15622222223--
226.DYR15713131313--
227.DYR158111111---
228.DYR15916-16---
229.DYR16013131313--
230.DYR161151515---
231.DYR162161616---
232.DYR16330303030--
233.DYR16425--25--
234.DYR16542434242--
235.DYR16611-1111--
236.DYR16711-1111--
237.DYR1686-66--
238.DYR1698-88--
239.DYR17038-3838--
240.DYR17144-44---
241.DYR17.112121212--
242.DYR17217-1717--
243.DYR17.213131313--
244.DYR173--2728--
245.DYR17.314141414--
246.DYR17413-13---
247.DYR17514-14---
248.DYR18.1101010---
249.DYR18.2-1014---
250.DYR1910101010--
251.DYR212121212--
252.DYR2010101010--
253.DYR23-1112---
254.DYR2612121212--
255.DYR27------
256.DYR2811111111--
257.DYR2911-11---
258.DYR310101010--
259.DYR30141414---
260.DYR317777--
261.DYR32------
262.DYR3314141414--
263.DYR35.19999--
264.DYR35.29999--
265.DYR36.14444--
266.DYR36.27777--
267.DYR38.111-11---
268.DYR38.212-12---
269.DYR3911111111--
270.DYR4012121212--
271.DYR4111-11---
272.DYR439999--
273.DYR44111111---
274.DYR45.110101010--
275.DYR45.211111111--
276.DYR45.315151513--
277.DYR469999--
278.DYR474444--
279.DYR4811111111--
280.DYR49------
281.DYR58-88--
282.DYR516666--
283.DYR529999--
284.DYR5410101010--
285.DYR5511111111--
286.DYR5616161616--
287.DYR5711111111--
288.DYR58.19999--
289.DYR58.211111111--
290.DYR59------
291.DYR615151515--
292.DYR6016161416--
293.DYR61------
294.DYR62------
295.DYR63.112121212--
296.DYR63.212121212--
297.DYR64.1------
298.DYR64.2------
299.DYR658888--
300.DYR66.110101010--
301.DYR66.210101010--
302.DYR67.19999--
303.DYR67.29999--
304.DYR67.311111111--
305.DYR67.411111111--
306.DYR68.19999--
307.DYR68.29999--
308.DYR68.313131313--
309.DYR68.413131313--
310.DYR69------
311.DYR714141414--
312.DYR7010101010--
313.DYR717777--
314.DYR7310101010--
315.DYR7411111111--
316.DYR75--1410--
317.DYR7614141414--
318.DYR7712121212--
319.DYR78------
320.DYR7916161616--
321.DYR811111111--
322.DYR806666--
323.DYR8134343434--
324.DYR8210101010--
325.DYR8313131313--
326.DYR8417171717--
327.DYR858888--
328.DYR877777--
329.DYR88.119-19---
330.DYR88.219-19---
331.DYR8911111111--
332.DYR9013131313--
333.DYR916666--
334.DYR9.11414-14--
335.DYR9212121212--
336.DYR9.21515-15--
337.DYR93131313---
338.DYR9410101010--
339.DYR957777--
340.DYR96777---
341.DYR9712121212--
342.DYR997777--
343.DYS44313131313--
344.DYS45311111111--
345.DYS4667777--
346.DYS46712121212--
347.DYS46818181818--
348.DYS46916151616--
349.DYS47011111111--
350.DYS47128282826--
351.DYS473------
352.DYS4748888--
353.DYS4758888--
354.DYS47611111111--
355.DYS4778888--
356.DYS47813--13--
357.DYS4808888--
358.DYS48413131313--
359.DYS48813131313--
360.DYS48911111111--
361.DYS49112121212--
362.DYS49310101010--
363.DYS496------
364.DYS4998888--
365.DYS5001313----
366.DYS5018-88--
367.DYS50213131313--
368.DYS50614141415--
369.DYS50710101010--
370.DYS50811111111--
371.DYS5091010----
372.DYS51211111111--
373.DYS51420202020--
374.DYS51612121212--
375.DYS51715151515--
376.DYS518-3334---
377.DYS5218888--
378.DYS52314141414--
379.DYS526A13-1313--
380.DYS526B37--37--
381.DYS527.134343431--
382.DYS527.235353534--
383.DYS528.118181818--
384.DYS528.219191919--
385.DYS5309999--
386.DYS53610-10---
387.DYS5389999--
388.DYS53910101010--
389.DYS54113131313--
390.DYS54215151515--
391.DYS54318181818--
392.DYS54414141414--
393.DYS54510101010--
394.DYS54616161616--
395.DYS547-4243---
396.DYS548------
397.DYS5508888--
398.DYS55113131313--
399.DYS5549999--
400.DYS558------
401.DYS559888---
402.DYS56220202120--
403.DYS56711-11---
404.DYS56911111111--
405.DYS571101010---
406.DYS57310101010--
407.DYS574101010---
408.DYS5779999--
409.DYS5799999--
410.DYS5809999--
411.DYS5818888--
412.DYS5828888--
413.DYS5838888--
414.DYS5848888--
415.DYS58510101010--
416.DYS58812121212--
417.DYS59211111111--
418.DYS5958888--
419.DYS59610101010--
420.DYS5987777--
421.DYS59922222222--
422.DYS60011111111--
423.DYS6089999--
424.DYS609------
425.DYS611161616---
426.DYS61231313131--
427.DYS6138888--
428.DYS6141818-18--
429.DYS6158888--
430.DYS61613131313--
431.DYS61812121212--
432.DYS619------
433.DYS6208888--
434.DYS6218-88--
435.DYS62219191919--
436.DYS6231091010--
437.DYS6249999--
438.DYS62533333333--
439.DYS62628282828--
440.DYS62729282929--
441.DYS629------
442.DYS63021212121--
443.DYS63110101010--
444.DYS633------
445.DYS6348888--
446.DYS6371111-11--
447.DYS63910101010--
448.DYS6428888--
449.DYS64418181818--
450.DYS6458888--
451.DYS6498888--
452.DYS651------
453.DYS655------
454.DYS65636-36---
455.DYS66288-8--
456.DYS6645050-50--
457.DYS6667777--
458.DYS6677777--
459.DYS6685555--
460.DYS6729999--
461.DYS6731111----
462.DYS6756666--
463.DYS67611111111--
464.DYS67711111111--
465.DYS67811111111--
466.DYS67913131313--
467.DYS6815555--
468.DYS68310101010--
469.DYS684575757---
470.DYS68538-38---
471.DYS68621202121--
472.DYS687363636---
473.DYS68878-78---
474.DYS6927777--
475.DYS6948888--
476.DYS69533323333--
477.DYS6967777--
478.DYS7015555--
479.DYS70229292929--
480.DYS70310101010--
481.DYS7055555--
482.DYS70615151515--
483.DYS70723-2323--
484.DYS70827272727--
485.DYS70920202020--
486.DYS71164-64---
487.DYS713414141---
488.DYS71814141314--
489.DYS71912121212--
490.DYS72033333233--
491.DYS72119191919--
492.DYS72222222222--
493.DYS72319191919--
494.DYS725.131--31--
495.DYS725.232--32--
496.DYS725.332--32--
497.DYS725.433--33--
498.G0941111111111--
499.L13133333--
500.L144444--
GENETIC DISTANCE
15/420
16/447
22/415
3/111
4/111
REFACTORED x/500181827--

GO TO TOP OF TABLE

Any one tester in a group, even if genealogically proved to be of the group, can have a higher than usual GD, especially when looking at a smaller number of STR markers. A higher marker count can provide more accurate averages. The 500 Big Y STRs, then, can be very useful when trying to determine an approximate relationship between two testers. This appears to have worked out well with the three Big Y testers in CF02.

Remember that the Nehemiah tester lacks three SNPs that are found to belong to Benjamin's descendants. This means that the MRCA for both groups lived much earlier and that Nehemiah's lineage branched off first. Note also that the modal is skewed toward Benjamin's own haplotype because most of the group members are his descendants. This means that Nehemiah's GD should be higher than that for Benjamin's descendants. And that's just what we found: both Benjamin testers (the first two columns) have a GD of 18 from the modal, but the Nehemiah tester has a GD of 27.

Let's take it a step further. Benjamin was born 336 years before the present era (standardized to be 1950). The average rate of mutation, then, for Ben's descendant's 18 mutations is just under 19 years. Multiply that by Nehemiah's GD of 27 and we have about 513 years to the MRCA, or roughly the year 1440. This could well be an exaggerated figure, but it's a start, and it works well with the three-SNP difference between the Benjamins and non-Benjamins.

 CDY Redux 

I'd mentioned in article 38 that a pattern is emerging with the two CDY markers. The values of 37/38 appear to indicate a lack of the three Benjamin SNPs. So far, that has borne out in four testers. There are a total of eight testers in CF02 who match this pattern. And there's circumstantial evidence in their genealogies that some of the lineages (except for Samuell and Nehemiah) originated in Goshen (Orange County), New York. I hope to have all of these tested by the end of summer.

Most FTDNA customers have tested for 37 STR markers. Indeed, I feel there's little advantage in doing 67 markers, and I've seen no evidence that 111 markers is much better. Naturally, there's a large difference between 37 and 500 markers. Still, FTDNA chose those 37 because they tend to display the most variety. (In other words, they've been shown to be a bit more fickle than the others.) Let's look at them in respect to the non-Benjamins, paying attention only to the area that shows genetic variation, loci 13-32.



There's one huge caveat that needs to be noted at this point. Each of these ancestors has only one tester. Any number of these mutations could have been acquired in the generations between the birth of the ancestor and that of the tester. Subsequent testing can alter the above table dramatically.

But if we take this at face value, Samuell and Nehemiah were not only distantly related from one another, it appears to have been true in their relationship to the other six testers listed above. Of those, Thaddeus and his father Jabez are believed to have gone west from the Goshen area. Abraham and Thadeus were brothers. They went to Virginia but are also thought to have been from Goshen. In any event, the GD among these six is very low. But here's the kicker, with the exception of the CDY markers, the STRs for the last six look very Benjamin-like.


<speculation>

What can this mean? STR mutations are sometimes associated with SNP mutations. This is the reason FTDNA can make predictions about haplogroups without testing any SNPs. I'm neither a chemist nor a geneticist, but I suppopse it's possible the three A12022 SNP mutations caused a disturbance in the area where the CDY markers reside. And this could have been a one-time event occurring not long before Benjamin was born. It would explain several things: that Benjamin and the ancestor of these "other" Cooleys were closely related to one another but less so to Samuell and Nehemiah; and that the "others" were not descended from Benjamin and, in fact, might have had an immigrant ancestor all their own.

Abraham has long been said to have been born in England. I discounted that once we saw that his STRs, and those of his brother Thadeus, are Benjamin-like. But what if the Goshen Cooleys were of a family that immigrated separately, perhaps in the mid- to late-seventeenth century? And what if their early records were lost, perhaps simply because the family broke up early on, some going west and others south? Perhaps that's why we've been unable to tie any of them together. That's a lot of speculation. But if the DNA evidence holds up, we could have something like this:



</speculation>

The more data we have, the better it can be developed. I'd first encourage all CF02 testers to test for the following SNPs: A12020, A12022, A12024, and Y23835. They can be had at FTDNA for $39 each and at yseq.net for $17.50 each. We also need more testers for Samuell and Nehemiah so that we can more accurately determine the genetic distance between what is now appearing to be four distinct groups: the Benjamins, the Samuells, the Nehemiahs, and the hypothetical Goshen, NY group.

I'm always available for questions.

1 Genetic Distance (GD) is determined by finding the accumulated absolute difference (-2 becomes +2) between each occurrence. Although I haven't confirmed with YFull, it looks to me that they simply summed the number of instances of differences.