Latest News

Release 34

Finally we have created a new release! 2.669 new haplotypes from 24 populations have been submitted. Among these are for the first time data from Israel, the Palestinian Authority Area and Sudan. Altogether, the Y chromosome database now presents 693 population studies from 105 countries. 6.245 haplotypes of now 89.237 are classified by Y-SNP analysis for the haplogroup. With 112 binary markers 116 branches of the Y chromosome phylogenetic tree were detected. Hence, already roughly a third of the published clades is represented by at least one sample in the YHRD.

Post Congress News

• The number of registrations (235 from 34 countries) and abstract submissions (97) for the 7th Y chromosome / 4th EMPOP workshop at 22.-24.April 2010 in Berlin reached an all-time high (Program and Abstracts). Sadly, the Eyjafjalla eruption stopped the flights of 90 guests from overseas, UK and some other European countries. Portraying human populations (with polymorphisms of Y, mt, X and autosomes), developing mathematical models for population dynamics and using this knowledge for applied sciences (as forensic genetics) is the perennial focus of this international gathering. The special workshop issue (published by Forensic Science International: Genetics) will present a selection of the 25-30 most interesting papers. The next workshop will take place 2012 in Porto (Portugal).

Information

The conference will be on schedule. All papers either presented in Berlin or not (due to the grounded air traffic) are eligible for publication in the special FSIG issue. Current situation (Wednesday, 10:00): Air safety officials of The German Air Traffic Control (DFS) agreed to lift volcanic ash restrictions on German airspace. Almost all airports (except Dresden, Leipzig, Erfurt and Münster) are operating. Please ask your flight company about the schedule of their flights.

Release 33

We have created release 33 (on March 3rd, which is 3.3. Hm?). 2521 new haplotypes, 1003 of these extended by phylogenetic markers have been added. The submissions stem from Albania, Angola, Benin, Brazil, Cote d'Ivoire, French Guiana, India, Italy, Romania, Russian Federation, Serbia and the United States. The YHRD now presents population studies from 102 countries (670 populations). Search Now! Contributions

• YA3019 by Leonor Gusmão, Verónica Gomes, Luisa Pereira, Cintia Alves, Antonio Amorim contributed to Cabinda, Angola [African]
• YA3447 by Gianmarco Ferri, Milena Alù contributed to Modena, Italy [Italian]
• YA3602 by Marius Bembea, Attila Patocs, Kinga Kozma, Claudia Jurca, Cristina Skrypnyk contributed to Tileagd, Bihor, Romania [Romani]
• YA3603 by Marius Bembea, Attila Patocs, Kinga Kozma, Claudia Jurca, Cristina Skrypnyk contributed to Palota, Bihor, Romania [German]
• YA3604 by Marius Bembea, Attila Patocs, Kinga Kozma, Claudia Jurca, Cristina Skrypnyk contributed to Sinteu, Bihor, Romania [Slovakian]
• YA3605 by Marius Bembea, Attila Patocs, Kinga Kozma, Claudia Jurca, Cristina Skrypnyk contributed to Oradea, Bihor, Romania [Romanian]
• YA3606 by Deborah A. Bolnick contributed to South Dakota, United States [Chippewa/Sioux]
• YA3607 by Deborah A. Bolnick contributed to Minnesota, United States [Chippewa]
• YA3608 by Deborah A. Bolnick contributed to Oklahoma, United States [Cherokee/Shawnee/Seminole/Creek/Choctaw/Chickasaw/Fox/Kickapoo/Cheyenne]
• YA3609 by Deborah A. Bolnick contributed to Wisconsin, United States [Chippewa]
• YA3610 by Nicolas Brucato contributed to Benin [Beninese]
• YA3611 by Nicolas Brucato contributed to Benin [Fon]
• YA3612 by Nicolas Brucato contributed to French Guiana [Noir Marron]
• YA3614 by Nicolas Brucato contributed to Cote d'Ivoire [Ahizi]
• YA3615 by Nicolas Brucato contributed to Cote d'Ivoire [Yacouba]
• YA3616 by Eugênio Nascimento, Eliana Azevedo, Eneida Cerqueira contributed to Bahia, Brazil [Admixed Brazilian]
• YA3617 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Jharkhand, India [Munda]
• YA3618 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Jharkhand, India [Sakaldwipi Brahmin]
• YA3619 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Madhya Pradesh, India [Gond]
• YA3620 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Madhya Pradesh, India [Kanyakubja Brahmin]
• YA3621 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Maharashtra, India [Konkanastha Brahmin]
• YA3622 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Maharashtra, India [Mahadev Koli]
• YA3623 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Punjab, India [Balmiki]
• YA3624 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Tamil Nadu, India [Iyengar]
• YA3625 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Tamil Nadu, India [Kuruman]
• YA3626 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Tripura, India [Riang]
• YA3627 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to Tripura, India [Tripuri]
• YA3628 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to West Bengal, India [Dhimal]
• YA3629 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to West Bengal, India [Paliya]
• YA3630 by Anil Kumar Sharma, Ikramul Haque, Soma Roy, Tania Ghosh contributed to West Bengal, India [Rajbanshi]
• YA3631 by Miljen Maletin, Igor Veselinovic contributed to Novi Sad, Serbia [Rusyn]
• YA3632 by Miljen Maletin, Igor Veselinovic contributed to Novi Sad, Serbia [Slovakian]
• YA3633 by Ville N. Pimenoff, Antti Sajantila contributed to Ural, Russia [Khant]
• YA3634 by Ville N. Pimenoff, Antti Sajantila contributed to Ural, Russia [Mansi]
• YA3635 by Gianmarco Ferri, Milena Alù contributed to Albania [Gabel Romani]
• YA3636 by Gianmarco Ferri, Milena Alù contributed to Albania [Gheg Albanian]
• YA3637 by Gianmarco Ferri, Milena Alù contributed to Albania [Tosk Albanian]
• YA3638 by Gianmarco Ferri, Milena Alù contributed to Albania [Jevg Romani]

Y-SNP Fact Sheets

The inclusion of Y-SNPs in the database stands for a new dimension of the YHRD 3.0 project and was well received by the user community. Now we implemented new fact sheets for markers and branches with definitions, sequences, maps and protocols (e.g. Branch Q-M3 or Marker M17). Search results are linked to the fact sheets. Here you can directly search for Y-SNP branches and Y-SNP markers.

Release 32

Within a month academic groups submitted 2.948 new haplotypes (897 extended by YSNP markers). From this data we created release 32 comprising more than 84.000 haplotypes, roughly 3.600 of these with haplogroup assignement. The new or updated submissions stem from Brazil, China, Colombia, Croatia, Panama, South Korea and Sweden. The YHRD now presents population studies from exactly 100 countries (634 populations). History needed? 10 years ago, in December 1999, the database had 2519 haplotypes from 21 European populations.

Y-SNPs and Release 31

With new release 31 the first 2.671 Y chromosomes (from 41 populations) become searchable not only for STRs but for phylogenetic Y-SNP markers and the assigned haplogroups. Since different groups use different SNP panels to define a branch of the phylogenetic tree, the complete Y phylogeny with all synonymous markers was programmed and the haplogroup designation is automatically generated from the ancestral/derived states of the analysed binary polymorphisms. Check out the new Y-SNP Search and the Y-SNP Grouping tools in the YHRD. The new release also launches a biostatistical Y-STR mixture tool based on the algorithm by Wolf et al. 2005, enabling the forensic analyst to interprete male/male mixtures with one or more possible contributors. The database gratefully received further submissions from groups in Argentina, China, Dubai, Iceland, India, Japan, Poland, Spain and Venezuela. Altogether 60 populations with 1952 haplotypes were added or updated. Five samples from Belarus which were erroneously doubled in the last releases of the YHRD were deleted (Brest, Homiel, Hrodna, Mahiliou, Viciebsk with 196 haplotypes). We call on all submitters to update their samples with Y-SNP information.

Workshop

Registration to the 7th Y User Workshop / 4th EMPOP meeting in Berlin, April 22th-24th, 2010 is now open. Please check out the announcement.

Release 30 is online!

August 21, 2009: We have updated the database and added 30 new or updated population samples with 4,405 haplotypes. Most of these new haplotypes have been typed in the 17 locus (YFiler) format. The YHRD has now 79,147 haplotypes, 21,800 of these with the maximal extension. The new population sets stem from 11 countries (Brazil, China, Colombia, Ecuador, India, Japan, Slovakia, South Korea, Spain, Taiwan and Ukraine). Y chromosomes from 96 countries are now represented in the YHRD. We thank all colleagues for their contributions: Luisa Diaz from Bogota, Colombia, Sharan Fung from Guangzhou, P.R.China, Ana Fernandez Santander from Madrid, Spain, Fang-Chin Wu from Taipeh, Taiwan, Teresina Palha and Sidney Santos from Belem, Brazil, Claudia Jannet Martin La Rotta from Bogota, Colombia, Natsuko Mizuno from Chiba, Japan, Nam Soo Cho from Daejeon, South Korea, Sergey Kravchenko from Kiev, Ukraine, Eva Petrejcikova and colleagues from Presov, Slovakia, Bhuvnesh Yadav from New Delhi, India and Maria Geppert from our group in Berlin, Germany. All contributors have passed QC and received YHRD accession numbers for each contributed population sample (YA003524-YA003553).

AMOVA Tool Failure

The software used for scheduling all AMOVA calculations didn't manage to clean up old and erroneous runs. In a result it wasn't possible to submit new calculations to the queue. We solved this issue today and encourage anybody to try again.

New Release 29!

June 12, 2009: We have updated the database and added 30 new or updated population samples with 2,687 haplotypes. Most of these new haplotypes have been typed in the 17 locus (YFiler) format. The YHRD has now 74,742 haplotypes in 565 populations, 23% (17,384) of these with the maximal extension. The new populations sets stem from 9 countries (Belarus, Brazil, Jordan, Maroc, Mexico, Russia, Sri Lanka, Taiwan, Uganda).

Update: Mutation rates and AMOVA

June 3, 2009: We have edited the Research page and included a comprehensive list of mutations and mutation rates per Y-STR locus as well as related information. Furthermore we improved the AMOVA calculation e.g. to allow the inclusion of population sets in your analysis. We switched from Kruskal's (Venables & Ripley 2002) to Sammon's formula (Sammon 1969) to calculate the MDS plot. The main difference between the two approaches is that Sammon's formula places more emphasis to small distances due to an additional normalization term.

De-bug release

March 23, 2009: Thanks to Mark Jobling, we were able to identify some duplicates of haplotypes with mutations at DYS385. There were 19 duplicates in the database:

Population	Removed duplicated haplotypes
Central Bohemia, Czech Republic [Czech]	1
Malaysia [Malay]	1
Bhutan [Bhutanese]	4
Malaysia [Han Chinese]	3
Taiwan [Han]	1
Minnan, China [Han]	1
Buenos Aires, Argentina [European]	1
London, United Kingdom [Indo-Pakistani]	1
Viet Nam [Vietnamese]	1
England-Wales, United Kingdom [Chinese]	1
Chengdu, China [Han]	2
Northern Portugal [Portuguese]	1
Berlin, Germany [German]	1
Sum	19

There were also 8 wrong assignements of samples with mutations. All populations were cross-checked with their original submissions and all invalid duplications were removed. For this we created a new release R28. This serious data error was caused by an unintentional import of two different versions of the old mutation table from YHRD 2.0 in July 2008. We apologize for that. Please contact us if you need more specific informations about affected haplotypes or populations.

New Release 27!

February 13, 2009: We have updated the database and added 19 new or updated population samples with 3,974 haplotypes. Most of these new haplotypes have been typed in the 17 locus (YFiler) format. The YHRD has now 72,082 haplotypes, 22% (15,956) of these with the maximal extension. The new populations sets stem from 6 countries (Greenland, Kuweit, Italy, Spain, Tunisia, United States of America). We thank all colleagues for their contributions: Carmen Tomas Mas, Charlotte Hallenberg and Niels Morling from Copenhagen, Denmark http://www.yhrd.org/YC000109, Arthur Eisenberg, Bruce Budowle, Lisa Calandro, Manohar Furtado from Quantico, Houston and Foster City, USA http://www.yhrd.org/YC000179, Achmed Rebai and Imen Ayadi from Sfax, Tunisia http://www.yhrd.org/YC000177 and Antonia Picornell Rigo from Palma de Mallorca, Spain http://www.yhrd.org/YC000178 All contributors have passed QC and received YHRD accession numbers for each contributed population sample (YA003475-YA003493).

New Release 26!

We have updated the database and added 16 new or updated population samples with 2,943 haplotypes. Most of these new haplotypes have been typed in the 17 locus (YFiler) format. The YHRD has now 68,108 haplotypes, 13,089 of these with the maximal extension. The new populations sets stem from 9 countries (Germany, Czech Republic, Greece, China, Poland, Brazil, Turkey, Italy and Argentina). We thank all colleagues for their contributions: Miguel Marino from Mendoza, Argentina, Jodi Irwin from AFDIL, Rockville, USA, Andrea Verzeletti from Brescia, Italy, Lu Di from Beijing, China, Nie Shengjie from Kunming, China, Daniel Vanek from Prague, Czech Republic, Paulina Wolańska-Nowak from Krakow, Poland, Omer Gokcumen from Ankara, Turkey, Jürgen and Lotte Henke from Cologne, Germany, Tadeusz Dobosz from Wroclaw, Poland, Rafal Ploski from Warsaw, Poland. All contributors have passed QC and received YHRD accession numbers for each contributed population sample (YA003461-YA003472).

Workshop History

Check out the chronicle of the Y User Workshops, a forum where analysts and renowned scientists gathered to discuss the theory, techniques and applications of Y-STR haplotyping from the very beginning. Y chromosome profiling is nowadays a well accepted method in forensics and anthropology with the YHRD database as a platform of many sampling projects, tools and documents. The 7th Forensic Y-User Workshop (in conjunction with the 4th EMPOP User meeting) will be held again in Berlin, Germany, 22-24 April 2010.

Website First Aid

Have you trouble using parts of the database? Do you observe unexpected results? Please follow these steps:

1. Check that all modern techniques needed to use this website are available: Tech Check. Please inform your local administrator about failing parts of this test.
2. Did you login before you started searching the database? Otherwise you'll be restricted to two searches, even if you got an account.
3. Please don't use the "Next" and "Back" buttons of your browser, it's likely to cause problems with integrated maps and AJAX requests.
4. Do you block ads? Please make sure that neither Google Analytics nor Google Maps are blocked.
5. Search in the Spam folder of your email account, when looking for missing activation/validation emails from the server.

If anything else, contact us.

Release 25 is out

We have updated and corrected the database and added 35 new population samples with 6,203 haplotypes. Most of these new haplotypes have been typed in the 17 locus (YFiler) format. The YHRD has now 65,165 haplotypes, 10,201 of these with the maximal extension. The new populations sets stem from 14 countries (Italy, Brazil, Morocco, China, South Korea, Iran, Azerbaijan, Costarica, Portugal, Namibia, Bangladesh, Algeria, Albania and Romania). We thank all colleagues for their contributions: Gianmarco Ferri from Modena, Luiz Fernando Jobim from Porto Alegre, Rachid Aboukalid from Rabat, Weiwei Wu from Hangzhou, Soon-Ja Kang from Seoul, Laurent Palet from Toulouse, Ivan Nasidze from Leipzig, Corné Hogerheijde from Amsterdam, Mónica Carvalho from Coimbra, Haruo Takeshita from Izumo, Sharif Akhteruzzaman from Dhaka, Carlo Robino from Torino and Florin Stanciu from Bucharest. All contributors have passed QC and received YHRD accession numbers for each contributed population sample (YA003437-YA003458).

Numbers

After being online for a month now, it's time summarize the use of the database with some numbers.

	Search Haplotypes	Calculate AMOVA
Overall	12.534	36
Registered users	2964	36
Number of unique users	183	13

• 42.061 site impressions
• 4.553 visits
• 2.010 unique visitors
• 355 registered users

• average CPU load 12% with a maximum of 77%
• average network load 1,03MB/s with a maximum of 41.46MB/s
• total bytes transfered 717.3MB

Third Rebirth

Please welcome our new baby! It was a lot of work, but finally the new system is here and is waiting for your Database Search or an AMOVA Calculation.