Hibernation, Metamorphosis, and Haplogroup J2 (M172)

Many of you might have noticed that not much has happened with the Haplogroup J2 project over the last 4 years. Some of you will remember a time when much work was regularly done on the J2 project, there were research goals and haplotype cluster & haplogroup subclade hypotheses, and there were updates every couple of weeks… Then nothing… Nothing for months… You might be wondering, – What happened?!…

In my masters thesis I studied snow tussock seed predation.  One of the insect seed feeders was the larvae of a “Fungus fly”.    After feeding on the seeds for a few weeks, the “grubs”would drop to the ground and would hibernate for some time.  When conditions were ideal,.. they would then pupate (just like a caterpillar sheds its skin and becomes a chrysalis).  Then,after metamorphosis it would emerge as an adult, and the life cycle would repeat.  Some times they might hibernate just a few months, other times environmental conditions might be so difficult, that it is safer for them to continue remaining hibernating for  more than a year (sometimes many years) before conditions are suitable for them to metamorphose, and emerge in their new form…..

….Wait,.. What has this got to do with Haplogroup J2?!?!

So, ..what has happened to the Y-DNA Haplogroup J2 project the last 4 years??
In a nut shell – Sir Nico, Earthquakes, and Hypodopaminergia … (with a dash of the EU financial crisis sprinkled in).

The “hibernation” of the Y-DNA haplogroup J2 project has now ended, – conditions are now such that I can now begin to initiate changes to move the project in a positive new direction….

Next year, the J2 haplogroup project will have a new structure and new member driven goals – there will be a team of  co-admins.  The old “Haplogroup J2 Y-DNA project” will have its original research goals answered and will be completed.  The FTDNA  J2 DNA group itself won’t end, – instead it will be transformed into effectively a new entity – the J-M172 project. The J-M172 project will “begin with a clean slate” so to speak, operated by a team of admins.  Some of these different co-admins will have their own speciality areas, that they are in charge of (eg. some people will be in charge of J2a-L24, some in charge of J2b etc…)…

Before this new J2 project incarnation can fully emerge, there will be a period of metamorphosis over the next few months.  Behind the scenes, this process has already begun.

You might ask, – why can’t the project transformation be done straight away?  Basically, – I first need to tie up all the old research “loose ends” for the J2 Y-DNA project. Specifically, the research goals of the original project will be answered via a giant haplotype analysis,

The appointing of co-admins will be a gradual process over the project metamorphosis period, rather than immediate.  There are a number of reasons for this, and the most salient reason is that the results of this analysis will determine what subgroups are used on the M172’s project’s pages.  Co-ordinating the responsibilities of the future full admin team will be more straightforward after the results categories are revamped (since different co-admins will be responsible for specific clades/subgroups).

You’ll see the project haplotype results here.  The default will be that all haplotypes are visible – if anyone for any reason doesn’t want their results publically viewable, – then please let me know…

Some of you might find that on the FTDNA site results tables, your haplotype is in a category that doesn’t make sense, and/or some haplotypes are categorised in an inconsistent manner.  There is a reason for this, and the results tables will be “straightened out” as part of the transition between the old project into the new project.

Many of the results are categorised into clusters that were defined in earlier J2 project analyses, and some of them might be currently in the wrong cluster.  Some of the old clusters now correspond to defined subclades and some of them now appear to be “artificial”clusters (ie. a mish mash of haplotypes that were once grouped together in the results of a “network diagram” analysis, but now don’t seem to be , or it’s uncertain if they are related or not).

All of this will be straightened out after the analyses are completed – in fact that is the aim of the analyses, – to find out whether we can develop a method to cluster haplotypes in a better way.  So what is a “better” way? – to get clusters correlate to subclades in the most accurate manner possible.

… so what is this analysis?!

The question being – Can extended haplotypes accurately predict subclades (which is actually a slightly more complicated question to answer than it would initially seem – the short answer is yes and no).

Most importantly, I want present these results in a manner that everyone can understand.  In a way, doing the research analysis is the easy bit – the hard thing, is translating it from statistical/phylogenetic mumbojumbo jargon into plain english.

The first part of the giant analysis was actually completed a couple of months ago, – what has been taking time, is figuring out the best way to present and explain the analysis, so that it is “crystal clear” and understandable to everyone.  I could present everything I’ve done in it’s present form, – but what is the point of doing that if it is incomprehensible to the average project member.I have been doing my best to think of the “ultimate” clearest analogies, to make everything as comprehensible as possible.

For instance,  compare the differences between the two cluster diagrams below:

Radial Cladogram comparison (neutral weighting v’s optimal mutation rate weighting)

….I could tell you that:

These two diagrams are constructed from the same haplotype data, with the only difference being that one of them has been weighted neutrally (correcting for the inherent character weighting derived from STR repeat ranges for markers) and the other one has characters weighted by an optimal mutation rate model – weighting for each marker determined from a predictive polynomial regression model constructed from comparing the marker mutation rate with how significantly different  the  allele distributions for that marker are between M410 and M102.

… but most people will be either thinking 😐 or 😯  To the average person ,…the above would be just as unintelligible if I had been speaking in Klingon (…and in fact, it probably would have been far more entertaining if I had written it in Klingon, …which incidentally sounds remarkably similar to my son’s speech…)…   It would be of more use to the average project member, if these esoteric ramblings were first demystified….

….  What I’m doing now is thinking of the best analogies to explain things in the clearest way possible.  I’m making diagrams, that will help clearly to explain the difference between haplotype clusters and haplogroup subclades.  I’m writing draft posts that explain what all of this is in plain English.   All of this has taken much more time than I originally assumed.  It’s all rather like my father clearing out his garage alcove –  to do “A” he first has to do z, before he can do y, before he can do x,…. etc…. What seems in theory to be a quick simple task,.. becomes a large detailed task, because of the very important preparation work that needs to be done first…

Building an awesome city on a swamp would all be to waste if the sufficient foundations aren’t put in first….just think what would happen if there was an earthquake…

…Wait … that sounds familiar…

Earthquake….. Christchurch…. Swamp…

So really,.. this post now is to let you know that – even though it seems like nothing is happening on the surface, – big things are happening behind the scenes.. it just takes a bit of time to figure out how to explain and present it best, so that it’s as understandable and relevant to everyone as it possibly can,.. (ie. not esoteric gibberish).

Basically,.. – before I present the results of the analyses I’ve been doing – I first need to explain:

1) Why am I doing this?

2) How is it relevant to the average haplogroup J2 person?

3) What is the difference between “clusters” and “clades” (and how do each of these relate to nomenclature, – ie. haplogroup names).

… and all three of these need to be explained in the clearest way possible.

I will begin to answer that in my next post, which should be in a couple of days…

Finally,.. I’d like this future new project to foster collaboration and unity between researchers.   I think it is very important to have several different speciality projects for the different subclades, – but it’s also important for all these different projects to link together in a collaborative network.  For instance, – I’ll be inviting people that are admins for different sub-clade projects to be a co-admin on this M172 project.  Some of these different co-admins will have their own speciality areas, that they are in charge of (eg. some people will be in charge of J2a-L24, some in charge of J2b etc…)…

Of course,.. – talk is well and good, but what counts is action.  This haplogroup J2 project revamp almost happened two years ago,. – but then the Christchurch earthquakes happened.   When hit by a continuing series of compounding disasters, the best intentions slip away…..

No,.. – they don’t slip away  – they are wrenched away by the stress and chaos as there was not one disaster, but many.  Just as you begin to pull your life together,  another large quake hits, and the regained order is shattered away, yet again.  Like a perpetual tectonic groundhog day.

The best of intentions that began to germinate – before the seismic series started – sit on the sidelines waiting, hibernating, until some sort of order in life is restored.  Not easy in a city that is broken, fragmented.  Nothing is “normal” any more…