[KerryOdair]

Very Nice presentation by Greg Magoon from Full Genomes:


'Next-Gen'
Y Chromosome Sequencing: Progress and Promise
2014 International Genetic Genealogy Conference
Washington, D.C. August 16, 2014
Greg Magoon

https://docs.google.com/file/d/0B8eigUEXUAvlMkFweDdHVzdMN2c/edit

[KerryOdair]

YTree v2.24 (in the process of calculating now...)
Statistics: 571 SNPs, 127 subclades.
By haplogroups:
C: 2 SNPs
E: 31 SNPs, 9 subclades
G: 3 SNPs, 2 subclades
H: 4 SNPs
I1: 73 SNPs, 15 subclades
I2: 143 SNPs, 28 subclades
J: 62 SNPs, 17 subclades
L: 51 SNPs
N: 28 SNPs, 4 subclades
Q: 57 SNPs, 6 subclades
R1a: 40 SNPs, 24 subclades
R1b: 79 SNPs, 22 subclades

[KerryOdair]

Update from Maximus Centurion
YFull.com: Y-Chr Sequence
Interpretation Service

YTree 2.25 (due date 15-20 October) coming soon...
1724 SNPs, 138 subclades:
C: 54 SNPs
E: 226 SNPs, 6 subclades
G: 83 SNPs
H: 3 SNPs
I1: 134 SNPs, 28 subclades
I2: 193 SNPs, 25 subclades
J: 84 SNPs, 1 subclade
L: 53 SNPs, 1 subclade
N: 163 SNPs, 16 subclades
O: 1 SNP
Q: 225 SNPs, 16 subclades
R1a: 313 SNPs, 24 subclades
R1b: 92 SNPs, 21 subclades
T: 92 SNPs, 4 subclades

[KerryOdair]

Statistics for the next version (2.27) of the Tree (coming soon...):
1192 SNPs, 205 subclades
by haplogroups:
A0: 106 SNPs
A1b1: 32 SNPs, 2 subclades
E: 70 SNPs, 9 subclades
G: 89 SNPs, 1 subclade
H: 1 SNP
I1: 122 SNPs, 44 subclades
I2: 273 SNPs, 29 subclades
J: 36 SNPs, 8 subclades
T: 49 SNPs, 6 subclades
N: 18 SNPs, 5 subclades
O: 185 SNPs, 27 subclades
Q: 38 SNPs, 7 subclades
R1a: 99 SNPs, 40 subclades
R1b: 72 SNPs, 27 subclades
others: 2 SNPs

[KerryOdair]

Statisctics for the next version 2.28 of our Y-Tree YFull (coming soon):
440 SNPs, 83 subclades
by haplogroups:
A0: 1 SNP
A1b1: 2 SNPs
E: 11 SNPs, 2 subclades
G: 14 SNPs, 1 subclade
I1: 52 SNPs, 15 subclades
I2: 64 SNPs, 10 subclades
J1: 4 SNPs, 3 subclades
J2: 48 SNPs, 1 subclade
T: 4 SNPs, 3 subclades
N: 8 SNPs, 9 subclades
O: 6 SNPs, 1 subclade
Q: 87 SNPs, 8 subclades
R1a: 44 SNPs, 12 subclades
R1b: 73 SNPs, 13 subclades
R-M479: 27 SNPs, 4 subclades
others: 5 SNPs, 1 subclade

[KerryOdair]

This certainly needs to be accomplished soon and adopted by both commercial, academic and private groups. These groups have tried to force their designations on other groups to the confusion of all.


Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era

H.D. Larmuseau Maartenemail, Van Geystelen Anneleen, Kayser Manfred, van Oven Mannis, Decorte Ronny
Received: July 30, 2014; Received in revised form: November 7, 2014; Accepted: November 9, 2014; Published Online: November 14, 2014
DOI: http://dx.doi.org/10.1016/j.fsigen.2014.11.012
Publication stage: In Press Accepted Manuscript
Abstract
Full Text
References
Highlights
•An overview of four defined categories of currently used Y-chromosomal phylogenies.
•A reduced consensus tree is the most appropriate reference resource for forensics.
•Initiatives to reach an international consensus phylogeny are highly recommended.
Abstract
Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended.

http://www.fsigenetics.com/article/S1872-4973(14)00252-X/fulltext

[KerryOdair]

Statistics for version 2.31 of Y-Tree is adding 321 SNPs, 22 subclades by haplogroups:

https://www.yfull.com

A1a: 1 SNP
B: 2 SNPs
E: 1 SNP, 1 subclade
H: 17 SNPs
I1: 21 SNPs, 2 subclades
I2: 51 SNPs, 1 subclade
J2: 38 SNPs
T: 96 SNPs, 6 subclades
N: 3 SNPs
R1a: 40 SNPs, 7 subclades
R1b: 50 SNPs, 5 subclades
others: 1 SNP

[KerryOdair]

New open source paper with supplemental files on:

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Abstract

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

http://mbe.oxfordjournals.org/content/early/2014/12/13/molbev.msu327.full

[KerryOdair]

This is information released by Yfull with version 3.4 of their Ytree which has age estimations for subclades and TMRCA. These will be refined over time with new samples. My particular results certainly are in line with previous estimations of time made independently by myself and others. This really is a significant step forward in dating the Y Chromosome with so many samples. Many thanks to the people at YFull. Below their statement on snp dating.


Vadim Urasin YFull.com: Y-Chr Sequence Interpretation Service


In the version 3.4 of Y-Tree we plan to show an estimation of age for all subclades with at least one Big Y or Y Elite. The algorythm of estimation by SNP count we will explain later in an article written by Adamov, Vladimir Gurianov, Sergey Karzhavin, Vadim Urasin We have checked our estimation by information of common ancestors our clients. For 12 of 14 subclades estimated age is inside 95% confidence interval. But estimated age of I-YP1012 and I-A379 is not. In the chart you can see all 14 subclades with known ancestors. For all subclades in the Y-Tree a confidence interval depends from number of samples. For subclades with 1 sample a bounds of 95% confidence interval of age estimation are -48.8% +61.6% in the average, for subclades with 2 samples a bounds of 95% confidence interval are -43.3% +50.1% in the average, for 3 samples: -34.6% +37,3%, for 4 samples: -28,9% +32,2%. More samples - better estimation

[KerryOdair]

Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data

Two important advances: 1) the accumulation of BigY and FGC test data, and 2) the publication of Y-chromosome sequences for three ancient samples (Anzick-1, Ust-Ishim, and K14), have made it possible to estimate the average rate of basesubstitutions (SNPs). The authors of this study have developed a new method of selecting true mutations in modern and ancient samples, and have defined with high accuracy the rate constant of SNP mutations: 0.82 · 10-9 per year per bp (95% CI: (0.70 - 0.94) · 10-9).


Link to paper:

http://rjgg.molgen.org/index.php/RJGGRE/article/view/151/175

[KerryOdair]

Here is an exchange with Yfull people on samples in their database on Facebook.

What is the total number of samples in the database today? This number would include all sources of sequenced data FullGenomes, FTDNA, 1000 Genomes Etc. Are there other sources besides the three I have named?

Vadim Urasin about 3300 samples. Almost all samples are from those 3 sources. Several samples are from scientific articles also. Version 3.9 of experimental tree to be released soon.

Also some stats from FullGenomes Folks

Here's our latest progress. Done by a team of 3 people.

Our latest numbers:

1. Total SNP discovery: 35,000 SNPs
2. Total FGC SNPs listed or in investigation status in ISOGG: 630
3. Total R1b SNPs from FGC in ISOGG: 133
4. Total FGC SNPs in YSEQ: 2,803 (as of April 14)
5. Total kits sequenced or analyzed: approximately 1,000 (10 mb (Big Y) or 14 mb (FGC/BGI)

The progress in the last 12 months has been amazing. A great deal of this effort is coming from the citizen scientists who are not waiting for the big companies to take some action to interpret the data.

[KerryOdair]

Full Text PDF and additional files available for viewing and downloading. We are progressing along nicely with research since this thread was first started. Thanks to this forum I believe we have received a much wider audience.

Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample

http://www.biomedcentral.com/1756-0500/8/174/abstract

Background Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. Methods DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. Results From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. Conclusions The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.

[KerryOdair]

Looking forward to seeing this paper when available. This is right in my wheel house dealing with the E haplogroup and the E-M35 subclade. This is what the sequencing of the Y is all about. Mr Cruciani is an author of this paper and has always been a leader in this kind of anaylsis. Really looking forward to reading this paper.

http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=fd6e251e-5448-4f9d-95cf-a1d3cef7476c&cKey=18c7dfd4-027e-49ae-90d3-b34103109e36&mKey=cabdedda-497c-457e-8481-34a866ab3681

[KerryOdair]

Nice to see that this issue is beginning to be addressed for other researchers. www.yfull.com is now up to version 3.12 of their database.

Data bank launched for global access to ancient DNA

Medical and other researchers and science teachers around the world will be able to compare ancient DNA from humans from thousands of years ago with the genetics of modern day humans, thanks to a new world-first open access databank at the University of Adelaide's Australian Centre for Ancient DNA (ACAD).

The Online Ancient Genome Repository (OAGR) (https://www.oagr.org.au/) catalogues a significant collection of DNA data from ancient human skeletons and microbes found in their dental plaque. Both raw and analysed data, along with details about the individual humans such as where they were found and how the data was produced, will be freely accessible in a searchable format.

Full Article

http://www.sciencedaily.com/releases/2015/06/150617091631.htm

Facebook page

https://www.facebook.com/ACAD.Adelaide?fref=ts

Another interesting ancient DNA Facebook page

https://www.facebook.com/groups/249055928471080/

[KerryOdair]

This was just published by YFull for SNP Lists

Full Y-SNP list now here - http://www.yfull.com/snp-list/
"Y" series - http://www.yfull.com/yf/snp-list/
"YP" series - http://www.yfull.com/yp/snp-list/