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Author: Dr John S Plant (bio)
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Initial Branching Model estimation for Main Plant Family

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Measuring more markers and their stability

The markers CDYa and CDYb, for example, are very fast changing (i.e. "unstable"). For the main Plant family, similar problems arise for the marker DYS456. Down the 700 or so years of the Plant surname these markers have occurred independently in different branches (i.e. so-called parallel mutations) and, on occasions, quite possibly changed back to an earlier value (back mutations). It is hence instructive to test the MEGA6 tree's resilience to omitting them.

  • The markers CDYa and CDYa are estimated to mutate at a rate of around 0.035 per generation giving a reasonable chance of a parallel mutation in each independent descent line of the surname. They can hence sensibly be omitted from "stable mutation" MEGA6 trees.
  • The marker DYS456 is said to mutate around four times more slowly than CDYa and CDYb. We omit it also from the "stable-marker" trees even though its mutation rate is similar to those of other markers that are used below as the "defining mutations" for some "major branches" of a tentative explicit descent tree. This is because of its very erratic behaviour in the main Plant family which may be due its very rare (0.1% and 1.6%) values (19) and (18), as well as less often (17) and (16) - it seems that these rare values might well be particularly unstable.
  • With the advent of Next Generation Sequencing, an indefinite number of Y-SNPs are likely to become available at a more affordable price and, as these are generally much more stable, they can be expected to determine the branching far more reliably.
The following diagram shows the 37-marker tree after these unstable markers have been omitted.

Stable 37 loci MEGA6 tree

Fewer men have been tested at the 67 marker level but their MEGA6 trees evidently add some further useful hints of genetic clustering. The changes in the Main Plant Family part of the MEGA6 trees, at both the 37 and 67 marker levels, can be summarised as follows.

37+ (with unstable markers)
(a) P1a, P1c, P33a and P23a
(b) P20a, P26a, PT3a
(c) P28a, P28b, P30a and P39a
(d) P2a, P36a and P43a
(e) PT1a, P19a perhaps linked also to P25a
(f) loose linkage of P7b, P29a
37- (without unstable markers)
(a) P1a, P1c, P23a, P33a tightly linked
(b)/(f) no mutations for P7b, P20a, P25a, P36a, PT3a
(c) P28a/b and perhaps also P30a and P43a
(d) no linkage remains for P2a, P36a
(e) PT1a, P29a and P19a
67+ markers
(a) only P1a tested and stands largely alone
(b) P20a, P26a, PT3a (P25a rather nearer (e))
(c) P28a, P30a
(d) only P36a tested and stands largely alone
(e) loose linkage of P19a, PT1a and perhaps P25a
(f) only P7b tested, loosely linked to P29a
67- markers
(a) only P1a tested and stands alone
(b) P20a,P25a, P26a, PT3a
(c) P28a, P30a
(d) only P36a tested and stands alone
(e) loose linkage of P19a, P29a and perhaps PT1a
(f) only P7b tested and stands alone
111 markers
As yet only 7 men tested, contribute little apart from a possible loose linkage of P7b, P36a in the 111+ MEGA6 tree

(67+) The following is the 67-marker MEGA6 tree with unstable markers

67 loci MEGA6 tree

(67-) The following is the 67-marker MEGA6 tree without unstable markers

Stable 67 loci MEGA6 tree

(111+) The following is the 111-marker MEGA6 tree with unstable markers. There are too few Plant men who have taken this test to expect more than one to share a well established branch. Tentatively however, in going from left to right, we might note that there is the most commonality before spliiting between P36a and P7b.

111 loci MEGA6 tree

It is clear that the above MEGA6 trees, which are based on relatively few men and limited Y-STR data, are not unique. Already, however, some parts of a Plant Y-STR descent tree seem more reliable than others. For example, we can tentatively identify the following groupings from the above MEGA6 diagrams.

Reasonably consistent
A: P1a, P1c, P23a, P33a from 37+(a) and 37-(a)
B: P20a, P25a, P26a, PT3a from 67+(b) and 67-(b)
C: P28a/b, P30a from 67+(c), 67-(c), 37+(c), 37-(c)
Less certain
D: P2a, P36a from 37+(d) (evidently also supported by shared ancestry)
D+: possibly add P7b to D from 111+
E: P19a, PT1a from 67+(e) and perhaps also P29a from 67-(e)

Building on these analyses, the following branching of the main Plant family has been adjudged, at least as an initial attempt at identifying the major branching. For the presentation of this descent tree, we have omitted some relatively unstable Y-STR markers (CDYa, CDYb and DYS456). Though this tree is at least useful for further discussion, it may be revised as more Y-DNA data become available for more markers and more Plant men.

Explicit Decent Tree based on Y-STR markers

At the top of the evident tree below, there is a Branch A (P23a-P1a-P1c-P33a) whose individuals share a (+1) mutation of DYS570: this mutation is then shown to be followed by no further mutation for P23a and different ones for each of P1a, P1c and P33a. The next grouping below in the diagram is defined by an early shared (+1) mutation of the marker DYS534 which identifies a P20a-P25a-P26a-PT3a branch (Branch B). In Branch C, P28a-P28b-P30a share the DYS385b(-1) mutation. Branch D has the DYS712(+1) mutatation (as well as the possibly stable value 17 of DYS456) for P2a-P36a-P7b. The bottom branch shares a DYS458(+1) mutation which might be a basis of a loosely-connected Branch E, with 3 or 4 further mutations occuring more recently for P29a and P19a.

Such branching helps to break down the abnormally large main Plant family into rather more manageable sub-populations. Further genealogical connections within these sub-populations can then be investigated using a combination of documentary and DNA evidence.

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