Best Wishes to all and keep up the great work.? Jim McCarthy? (Heading in the direction of 80 years old and in awe of the young brilliant people working on the project and led by the ever young Nigel McCarthy)
Thanks Elizabeth,
It is good to see James' input again.??
/r
Rusty Sullivan
Hello, Everyone.
Some of you may have noticed that there has been a quiet change of leadership in our R1b-CTS4466 Plus project.? I have retired as team leader of our great team and moved myself to a Co-Administrator role.?
Paul O'Donnell has graciously assumed the role of team leader to carry us forward.? We are all delighted that he has accepted the challenge.? We are in able hands.
You will have been notified that James Kane has returned to the team.? As far as I'm concerned, we have the best team in the World!
I hope to send an email to the whole project shortly.
Best Wishes,
Elizabeth
|
Re: Claristown 14/CT14 - R-A151 high profile cairn burial. WAS: Re: Vikings may not be who we thought they were, DNA study finds
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John,
I apologize for bringing up such an old post, but I HAD to respond to this one as somehow I missed this post this last year.? ?Since this is another R-A151 individual, (and potentially distant family for us A151 folks), I spent several days researching the burial to see what kind of details I could find out, as you can tell a lot about a persons life by how they are laid to rest.? ?After a wild goose chase, I narrowed down the source for Claristown 14 to a series of excavations and archaeological digs that were done in preparation for a new M1 motorway bypass around Drogheda, in Co. Meath, Ireland.? ??
The source record for the original DNA source & excavation was traced back to an excavation by Ian Russell in 2001.? ?Excavation details:? ?Burial 14, Skull. Site No. 0086. F401?Reg No. -?Habitat: R19.P3.S2?Lic No. 01E039? ?Description: Skull? ??Burial description:? ?Lintel grave within ring ditch
If anyone else is interested, this appears to be the article in?which CT14's excavation occurred..? I am still searching for this one as I would really like to read it in full:
Russell, Ian et al. - Claristown 2: a cemetery and later cairn; excavations for the Drogheda Bypass - M1 Motorway [paper to M1 Seminar, Drogheda, June 2001], XIII (2002) 23–31
In looking for further information, I found the M1 Motorway bypass summary findings has quite an amazing analysis of what was found at Claristown.? ?The burial process indicated that CT14, (if he is the man found in the center of this cairn) was a person of great importance!
Late Iron Age Roundhouse and Ring-Cairn
"Underneath a tree planted on a clearance cairn in Claristown a Late Iron Age roundhouse was discovered that had been transformed into a Late?Iron Age - Early Medieval ring-cairn monument.This?stunning site was set in the middle of a plateau,?centrally placed between the Nanny and DelvinRivers looking out towards the Irish Sea. The?roundhouse was probably built around 100 – 50 BC?with four concentric rings of posts. It was 11.58 m in?diameter, had an external drip gully and a porch-hall?entrance faced east. Inside, partition walls defined a?probable sleeping room, a small ‘waiting room’, a large empty ‘audience chamber’, and a cooking area seen by three hearths. In the possible ‘sleeping room’ a centrally placed sunken hearth contained a buried human infant, dating from first to fourth century AD. The building remained in use for several hundred years until around AD 300 – 400, when it was demolished and a circular layer of stones was laid where the building had stood.Through this platform base, a large stone-lined and stone-filled burial pit was sunk, containing a large human adult male, laid supine, east to west with the head to the west in a very Christian manner.
A huge bonfire was then made on the stone platform and many finds and animal bones show a great gathering and much feasting. After this the monument was created by digging a circular trench to contain a palisade made of paired posts and possible wattling.? The palisade appeared to act as a revetment holding?back an external bank or ring-cairn of stones. Inside?the palisade a small central cairn was thrown up. There are obvious similarities in both date and construction between Claristown and the Royal Site at Navan Fort (Site B), Co. Armagh.Was there a similarity in status and function?
During the fourth and fifth centuries AD nine Christian style human burials were set immediately outside the main ring-cairn.There were two doublemale burials, both covered with mounds of stone.Two pieces of clear glass, possibly Roman imports, were recovered."
I will be looking for the article written about the findings, as I want to confirm which individual is CT14.? ?Based on the descriptions from the source material for Lara Cassidy's paper, CT14 should be our man in the cairn...
John James
Mesa, AZ
|
Claristown 14/CT14 - R-A151 high profile cairn burial. WAS: Re: Vikings may not be who we thought they were, DNA study finds
John,
I apologize for bringing up such an old post, but I HAD to respond to this one as somehow I missed this post this last year.? ?Since this is another R-A151 individual, (and potentially distant family for us A151 folks), I spent several days researching the burial to see what kind of details I could find out, as you can tell a lot about a persons life by how they are laid to rest.? ?After a wild goose chase, I narrowed down the source for Claristown 14 to a series of excavations and archaeological digs that were done in preparation for a new M1 motorway bypass around Drogheda, in Co. Meath, Ireland.? ??
The source record for the original DNA source & excavation was traced back to an excavation by Ian Russell in 2001.? ?Excavation details:? ?Burial 14, Skull. Site No. 0086. F401?Reg No. -?Habitat: R19.P3.S2?Lic No. 01E039? ?Description: Skull? ??Burial description:? ?Lintel grave within ring ditch
https://docs.google.com/spreadsheets/d/1mk9pMMUbChzyW8CwVUYgokVL4iv83WBAKdIf3pWXJnw/edit#gid=833626537
If anyone else is interested, this appears to be the article in?which CT14's excavation occurred..? I am still searching for this one as I would really like to read it in full:
Russell, Ian et al. - Claristown 2: a cemetery and later cairn; excavations for the Drogheda Bypass - M1 Motorway [paper to M1 Seminar, Drogheda, June 2001], XIII (2002) 23–31
In looking for further information, I found the M1 Motorway bypass summary findings has quite an amazing analysis of what was found at Claristown.? ?The burial process indicated that CT14, (if he is the man found in the center of this cairn) was a person of great importance!
Late Iron Age Roundhouse and Ring-Cairn
"Underneath a tree planted on a clearance cairn in Claristown a Late Iron Age roundhouse was discovered that had been transformed into a Late?Iron Age - Early Medieval ring-cairn monument.This?stunning site was set in the middle of a plateau,?centrally placed between the Nanny and DelvinRivers looking out towards the Irish Sea. The?roundhouse was probably built around 100 – 50 BC?with four concentric rings of posts. It was 11.58 m in?diameter, had an external drip gully and a porch-hall?entrance faced east. Inside, partition walls defined a?probable sleeping room, a small ‘waiting room’, a large empty ‘audience chamber’, and a cooking area seen by three hearths. In the possible ‘sleeping room’ a centrally placed sunken hearth contained a buried human infant, dating from first to fourth century AD. The building remained in use for several hundred years until around AD 300 – 400, when it was demolished and a circular layer of stones was laid where the building had stood.Through this platform base, a large stone-lined and stone-filled burial pit was sunk, containing a large human adult male, laid supine, east to west with the head to the west in a very Christian manner.
A huge bonfire was then made on the stone platform and many finds and animal bones show a great gathering and much feasting. After this the monument was created by digging a circular trench to contain a palisade made of paired posts and possible wattling.? The palisade appeared to act as a revetment holding?back an external bank or ring-cairn of stones. Inside?the palisade a small central cairn was thrown up. There are obvious similarities in both date and construction between Claristown and the Royal Site at Navan Fort (Site B), Co. Armagh.Was there a similarity in status and function?
During the fourth and fifth centuries AD nine Christian style human burials were set immediately outside the main ring-cairn.There were two doublemale burials, both covered with mounds of stone.Two pieces of clear glass, possibly Roman imports, were recovered."
I will be looking for the article written about the findings, as I want to confirm which individual is CT14.? ?Based on the descriptions from the source material for Lara Cassidy's paper, CT14 should be our man in the cairn...
John James
Mesa, AZ
|
Thanks Elizabeth,
It is good to see James' input again.??
/r
Rusty Sullivan
Hello, Everyone.
Some of you may have noticed that there has been a quiet change of leadership in our R1b-CTS4466 Plus project.? I have retired as team leader of our great team and moved myself to a Co-Administrator role.?
Paul O'Donnell has graciously assumed the role of team leader to carry us forward.? We are all delighted that he has accepted the challenge.? We are in able hands.
You will have been notified that James Kane has returned to the team.? As far as I'm concerned, we have the best team in the World!
I hope to send an email to the whole project shortly.
Best Wishes,
Elizabeth
|
Hello, Everyone.
Some of you may have noticed that there has been a quiet change of leadership in our R1b-CTS4466 Plus project.? I have retired as team leader of our great team and moved myself to a Co-Administrator role.?
Paul O'Donnell has graciously assumed the role of team leader to carry us forward.? We are all delighted that he has accepted the challenge.? We are in able hands.
You will have been notified that James Kane has returned to the team.? As far as I'm concerned, we have the best team in the World!
I hope to send an email to the whole project shortly.
Best Wishes,
Elizabeth
|
Re: YDNA Warehouse STR Uploads and Updates
i did this but the website doesnt generate any sort of message acknowledging anything.? hopefully it went in
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Re: Heat Maps & Surname Tag Clouds
Thank you so much. This is so interesting. I found my Henry father-in-law on the map, kit # 69621, says he was from Coleraine, which is what the family history says. Many thanks. Charlotte Henry Hughes
On Saturday, July 16, 2022 at 10:21:19 PM EDT, James Kane <jkane@...> wrote:
There are some BETA quality changes on my experimental tree now:
1) You can search by known SNPs in a block as well as the Branch name.
2) The Locales... button will reveal a heat map of the most distant known ancestor's birth location. ?I plan to make this recenter on the centroid of geolocations, but the trigonometry is more than I am up to at this point today.
3) The Surnames... button will render a Tag Cloud of the surnames below the subclade you're viewing. ?Every time you hide or reveal the widget, it will rearrange a bit.
I expect there are a few bugs synchronizing the three functions, but it's 90% functional.
Remember that the heat map is only a representation of where someone typically in the last 300 years was born. ?It probably isn't very useful in divining the most probable location for origin.
Let me know if there are comments or feedback.
Thanks,
James Kane
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Re: Heat Maps & Surname Tag Clouds
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Re: Heat Maps & Surname Tag Clouds
is there a link?
Probably a good feature would be showing ancestors from other people that were dna matches with that have people living in the same area within (100 years?)
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Re: YDNA Warehouse STR Uploads and Updates
add my stuff also,? ill try and get the bam file.? after the hundreds of dollars i've spent you would think this comes with it
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Re: YDNA Warehouse STR Uploads and Updates
I recorded a quick 3 minute demonstration of how-to upload the STR CSV from FTDNA. ?It's pretty raw and the audio is janky, but it serves the purpose until I can go retrieve my audio recording gear from storage.
Hopefully this helps the more audio/visual learners.
Thanks,
James
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Re: YDNA Warehouse STR Uploads and Updates
James, on you go, you've got my consent - I've joined all these projects to get results, share with others and build something for the future - if this helps you/us and the rest of CTS4466, I'm in.??
Slan
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Hi Nigel, Phil Millar (PJRM) here - FTDNA Kit No: B654981?-
an Admin, with my permission, when I was first joining projects, uploaded my file to the YDNA Warehouse, my Haplogroup is R-BY186342 but I think they've got me as an upstream subclade R-A6526, my family we're from Ulster (Northern Ireland) Antrim. Nigel, do
you have access to my file at YDNA Warehouse, if you don't, do I need to enable something, so you can? Nigel, just let me know what I need to do, to help you. Adh mor ort agus oiche mhaith.
Phil
When it comes to the Warehouse the Administration side of things are sparse. ?This will change over time as I build out tools to complement projects.
At the moment you have two files uploaded:
?sample_id | ? test? ? | filetype?
-----------+-----------+----------
?B654981 ? | Big Y-700 | vcf
?B654981 ? | Big Y-700 | bed
Either Garth needs to upload the STR CSV, or I can also use my roles as the YDNA-Warehouse Super User and a CTS4466+ Co-Admin to do it with your consent.
Thanks,
James
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Re: YDNA Warehouse STR Uploads and Updates
Hi Nigel, Phil Millar (PJRM) here - FTDNA Kit No: B654981?- an Admin, with my permission, when I was first joining projects, uploaded my file to the YDNA Warehouse, my Haplogroup is R-BY186342 but I think they've got me as an upstream subclade R-A6526, my family we're from Ulster (Northern Ireland) Antrim. Nigel, do you have access to my file at YDNA Warehouse, if you don't, do I need to enable something, so you can? Nigel, just let me know what I need to do, to help you. Adh mor ort agus oiche mhaith.
Phil
When it comes to the Warehouse the Administration side of things are sparse. ?This will change over time as I build out tools to complement projects.
At the moment you have two files uploaded: ?sample_id | ? test? ? | filetype? -----------+-----------+---------- ?B654981 ? | Big Y-700 | vcf ?B654981 ? | Big Y-700 | bed
Either Garth needs to upload the STR CSV, or I can also use my roles as the YDNA-Warehouse Super User and a CTS4466+ Co-Admin to do it with your consent.
Thanks,
James
|
Heat Maps & Surname Tag Clouds
There are some BETA quality changes on my experimental tree now:
1) You can search by known SNPs in a block as well as the Branch name.
2) The Locales... button will reveal a heat map of the most distant known ancestor's birth location. ?I plan to make this recenter on the centroid of geolocations, but the trigonometry is more than I am up to at this point today.
3) The Surnames... button will render a Tag Cloud of the surnames below the subclade you're viewing. ?Every time you hide or reveal the widget, it will rearrange a bit.
I expect there are a few bugs synchronizing the three functions, but it's 90% functional.
Remember that the heat map is only a representation of where someone typically in the last 300 years was born. ?It probably isn't very useful in divining the most probable location for origin.
Let me know if there are comments or feedback.
Thanks,
James Kane
|
Re: YDNA Warehouse STR Uploads and Updates
Hi Nigel, Phil Millar (PJRM) here - FTDNA Kit No: B654981?-
an Admin, with my permission, when I was first joining projects, uploaded my file to the YDNA Warehouse, my Haplogroup is R-BY186342 but I think they've got me as an upstream subclade R-A6526, my family we're from Ulster (Northern Ireland) Antrim. Nigel, do
you have access to my file at YDNA Warehouse, if you don't, do I need to enable something, so you can? Nigel, just let me know what I need to do, to help you. Adh mor ort agus oiche mhaith.
Phil
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Show quoted text
James,
?
Amazing progress, as your interventions always are! As you are aware I have been indicating postulated ancestral values at each tree branch on my Irish Type II / CTS4466 (and other haplogroup) trees all along, and since 2019 for several these trees have included
the 727 markers for which FTDNA extracts data from Big Y tests. Apart from downloading the .csv files to a single massive spreadsheet, my methods are laboriously non-computerised, I.e. mutations are identified by visual inspection of the data. I recognise
that universal application of such analysis needs a method such as yours.
?
Since I use the output from this exercise to estimate the age at each tree branch it is important that my identification of mutations is close to being correct.
?
I’m sure that comparison with your YDNA Warehouse results will cause me to rethink placement of some of the mutations I have postulated. I am equally sure that I will argue, based on logic rather than your program, that some of your conclusions cannot be correct.
Will you have an override facility which can be applied if you are in agreement with me (if ever you have time to review such cases in depth!)?
?
My own work has identified a number of independent levels on the trees which are defined solely by STR mutations, as would be expected. A few of these, early on, are particularly significant (e.g. FTY1172 on sheet 5 of the Irish Type II tree).Will the Warehouse
trees have similar characteristics, or will STR mutations only be marked as coincident with SNPs?
?
(I still await a response from Michael Sager to comments on FTDNA’s mew ‘Discovery’ tree node age estimates).
?
Nigel
Sent from for Windows
?
?
Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels. ?We will be using these to compute the ancestral values at each tree branch and adding them to the
. ?Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates. ?I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m. ?These samples along with 1000 other fairly random ones
are running through??to begin constructing a tree using this data. ?As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession. ?Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email. ?We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future. ?This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
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Re: YDNA Warehouse STR Uploads and Updates
James, Both of my cousins have done the Big-Y DNA. I'm not sure if I sent the raw data to you or if you need it?? Gordon Shuckrow, Jr. (FTDNA kit #424423) William Chance Shuckrow (FTDNA kit #MK66026)
I've also been in contact with Michael Power (adopted) and his bio dad John Sugrue, Sr. of County Cork, Ireland. They have both done FT Y67-DNA that is a match at one distance to Gordon Shuckrow. Unfortunately, Michael died unexpectedly from cancer but his bio dad is still alive. I'm in contact with Michael's widow.
Please advise if I need to do anything now, Sue
On Fri, Jul 15, 2022 at 3:22 PM James Kane < jkane@...> wrote: Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels.? We will be using these to compute the ancestral values at each tree branch and adding them to the .? Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates.? I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m.? These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data.? As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession.? Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email.? We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future.? This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
-- Enjoy a great day, Sue Severson 67 Martha Road, Orinda, CA 94563
925-255-7570
|
Re: YDNA Warehouse STR Uploads and Updates
Hi, ? I manage my deceased father’s DNA and had the Big Y DNA performed. His name is Richard McAvoy. I am not sure what results you have. I do not know what a BAM is and if you have my father's BAM. I have attached the his Big Y STR CSV.? Thanks, Marcia McAvoy
On Jul 15, 2022, at 6:22 PM, James Kane <jkane@...> wrote:
? Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels. ?We will be using these to compute the ancestral values at each tree branch and adding them to the . ?Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates. ?I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m. ?These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data. ?As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession. ?Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email. ?We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future. ?This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
|
Re: YDNA Warehouse STR Uploads and Updates
Will you have an override facility which can be applied if you are in agreement with me (if ever you have time to review such cases in depth!)? Yes, eventually. ?I am on and off working on a set of editing tools for the tree. ?Each branching block notes the changes from its parent block. ?The state changes can be SNPs, INDELs or STRs. ? ?Way down the road I’d also like to include a concept like a person as well for proven lineages. ?The state changes can be redefined manually in the report that renders the tree in your browser.
The intent is to allow a team to fix the tree’s mistakes and make further refinements manually.
Will the Warehouse trees have similar characteristics, or will STR mutations only be marked as coincident with SNPs? Yes, covered by the above functionality. ?A new Block with the STR mutation could be inserted between existing SNP block. ?I already do this with INDELs , since including them is an NP-hard problem for the current machine learning solutions.
Thanks,
James
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Re: YDNA Warehouse STR Uploads and Updates
Checking if the warehouse has the BAM: 1) Log in to YDNA Warehouse and click the Manage button on the test Subject. 2) Find the Big Y test kit data and click the Manage button. ?You will see a screen like this.  3) If you see any file called chrY.bam, chrYM.cram or callable_status.bed, you are good! ?No action is needed. The BAM/CRAM file just might not be re-uploaded yet. If you only see the files pictured above, a BAM file hasn't been submitted. 4) Open your FTDNA account in another browser window and navigate to your Big Y results page. 5)?Click the blue Download Raw Data button. This will open a modal dialog box with a privacy information statement. 6)?Click the green Share button to access a file download URL token. 7)?Copy the token into the "Retrieve file from Cloud service" box. The link will be nearly 500 characters long. 8) Click the Retrieve file button. The BAMs are typically processed in 72 hours and this page gets some additional tabs with analysis information. Thanks for the question. James Kane PS: ?If you have one of those very long Kit# as shown above and would prefer having your FTDNA kit # there message me directly with what it should be changed to.
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Re: YDNA Warehouse STR Uploads and Updates
how do i provide a BAM if that is needed?
dave
|
lilwayne
Phil Millar