Databases were accessed on July 13^th 2012

TABLE 1. Basic information on online databases for mtDNA polymorphisms in human populations. To avoid the risk of overloading the analysis with redundant and not validated data, we have not taken into account databases hosting data produced by single laboratories.

DATABASE PUB. ONLINE LAST UPDATE USER HELP REFERENCES CONTACT DNA-Fingerprint1,2 2004 n.a. x3 - info@familytreedna.com; thomas@dna-fingerprint.com Empop 2006 04/2012 x Parson & Dür, 2007 walther.parson@i-med.ac.at Family Tree Dna 2000 07/2012 x - info@familytreedna.com GOBASE 1996 06/2012 x O’Brien et al., 2009 gobase@BCH.UMontreal.CA HmtDB n.a. 06/20124 x Attimonelli et al., 2005 marcella.attimonelli@uniba.it HVRbase++ 1998 06/2005 x Handt et al., 1998; Burckhardt et al., 1999; Kohl J et al., 2006 arndt.von.haeseler@univie.ac.at Mitosearch2,5 2004 n.a. x - info@familytreedna.com MitoVariome 2009 07/2009 x Lee et al., 2009 yslee@kribb.re.kr mtDB 2000 03/2007 - Ingman & Gyllensten, 2006 Max.Ingman@genpat.uu.se mtDNA Community6 2012 09/2012 - Behar et al., 2012 media@familytreedna.com mtDNA manager n.a. 10/2011 x Lee et al., 2008 kjshin@yuhs.ac mtSNP database 2003 01/2006 - Tanaka et al., 2004 mtsnp@giib.or.jp  PhyloTree 2008 05/2012 - van Oven & Kayser, 2009 m.vanoven@erasmusmc.nl SMGF7 1999 07/2012 x - info@smgf.org     1 users may modify their own entries. 5 accepts data from Genographic users. 2 exchanges data with Family Tree DNA. 6 accessed on 20/09/2012 3 x stands for presence of a specific feature. 7 Sorenson Molecular Genealogy Foundation 4 Personal communication, M. Attimonelli.

 

TABLE 2. Basic information on online databases for Y chromosome polymorphisms in human populations. To avoid the risk of overloading the analysis with redundant and not validated data, we have not taken into account databases hosting data produced by single laboratories.

DATABASE PUB. ONLINE LAST UPDATE USER HELP REFERENCES CONTACT DNA-Fingerprint1,2 2004 n.a. x3 - info@familytreedna.com; thomas@dna-fingerprint.com Family Tree DNA 2000 07/2012 x - info@familytreedna.com SMGF4 2004 03/2011 x - smgfsupport@ancestry.com US Y-STR Database 2006 01/2012 x Ge et al. 2010 lfatolit@mail.ucf.edu Y-Filer Haplotype Database n.a. n.a. x - n.a. YHRD5  2001 02/2012 x Willuweit & Roewer, 2007 s@rprojekt.org  Ysearch 2003 n.a. x - ysearch@usernet.com     1 users may modify their own entries. 4 Sorenson Molecular Genealogy Foundation 2  exchanges data with Family Tree DNA. 5 Y chromosome Haplotype Reference Database 3 x stands for presence of a specific feature.

 

APPENDIX 1A. Information on polymorphisms and data source available in online databases for mtDNA polymorphisms in human populations.

Polymorphism Database HVRI HVRII Coding Region Whole Genome Data source Overlap with NCBI1 DNA-Fingerprint  1303 1303 - - Samples sent from individual donors - Empop 17321 17321 - - Literature and unpublished data2 p3 Family Tree Dna 146153 642214 193244 - Samples sent from individual donors5 p GO Base - - - 2714 Literature p HmtDB - - 975 8813 Literature c6 HVRbase++ 13873 4940 - 1376 Literature p MitoSearch 44741 155554 - - From various companies7 n.a. MitoVariome - - - 5344 Literature c mtDB - - 839 1865 Literature c mtDNA Community - - - 13492 Literature and unpublished data p mtDNA manager 9294 9294 - - Literature p mtSNP database - - - 1736 Literature c PhyloTree - - 943 14508 Literature p SMGF 75406 75406 - - Samples sent from individual donors n.a.               1Using an ad hoc mitomap link, GenBank was found to include a total 16,414 complete DNA sequences (Database accessed on 20/09/2012). The number of HVR-1 and HVR-2 data available cannot be reliably calculated. 2 Most sequences are based on raw data, not (only) literature (W. Parson, personal communication). 3  p stands for partial overlap. 4  Personal communication, B. Greenspan. 5  Includes individual data from the Genographic project. 6  c stands for complete overlap. 7 SMGF, Family Tree, Ancestry, Genographic and others unspecified.

 

APPENDIX 1B. Downloading and uploading from online databases for mtDNA polymorphisms in human populations.

Database Downloading  file format Uploading  population data file format DNA-Fingerprint  p1 ns2 - - Empop - - x3 Empop Family Tree Dna4   p  ns - - GO Base x Fasta - - HmtDB x Fasta - - HVRbase++ x Various formats5 - - MitoSearch x ns - - MitoVariome x Fasta - - mtDB x Fasta - - mtDNA Community x ns x ns mtDNA manager p  ns - - mtSNP database x Fasta - - PhyloTree x Fasta - - SMGF - - - -           1 p stands for the possibility to download only partial data. 2  ns, non specific; no formally defined format was used. 3  ns, non specific; no formally defined format was used. 4  Data from Genographic project may be uploaded. 5  Fasta, Genbank, HTML, Metadata, Phylip, TSV, XML

 

APPENDIX 1C. Matching and other tools available in online databases for mtDNA polymorphisms in human populations.

Match Database Complete Partial Range Other population genetics tools DNA-Fingerprint  x1 - - - Empop x x x Drawing quasi-median network Family Tree Dna - - - - GO Base - - - - HmtDB - - - Haplogroup predictor HVRbase++ - - - Newick-tree viwer, convert numbering MitoSearch x - - - MitoVariome - - - - mtDB - - - - mtDNA Community x - - FastmtDNA, mtDNAble mtDNA manager x x x Haplogroup estimation, match probability mtSNP database - - - mtSNP statistics PhyloTree - - - - SMGF x x x -   1 x stands for presence of a specific feature

 

APPENDIX 1D. Filters in online databases for mtDNA polymorphisms available in human populations.

Sample information Database Mutation In/Del HG Reference Geographical location Accession number Disease State Gender Age Tissue Multiple Queries DNA-Fingerprint  - - x1 - x - - - - - x Empop x x - x x x - - - - x Family Tree Dna - - t2 - t - - - - - - GO Base - - x x - x x - - - x HmtDB x x x x x x x x x x x HVRbase++ x - x x x - - - - - x MitoSearch - - x - x - - - - - x MitoVariome - - x - x x - - - - x mtDB - - - t t t - - - - - mtDNA Community x - x - - x - - - - - mtDNA manager - x - - x - - - - - x mtSNP database x x - x x x - x x x x PhyloTree - - - t - - - - - - - SMGF - - - - - - - - - - -                         1  x stands for presence of a specific feature. 2  t stands for reference table.

 

APPENDIX 2A. Information on polymorphisms and data source available in online databases for Y chromosome polymorphisms in human populations.

polymorphism Database STR haplotypes STR/SNP haplotypes Data source DNA-Fingerprint  1305 114 Samples sent from individual donors Family Tree DNA 236302 627951 Samples sent from individual donors2 SMGF 38447 - Samples sent from individual donors US Y-STR Database 18719 - From various laboratories3 Y-Filer Haplotype Database 11393 - n.a. YHRD 101055 9039 Literature and unpublished data Ysearch 112513 - From various companies         1 Personal communication, B. Greenspan. 2 Includes individual data from the Genographic project. 3  National Center for Forensic Science, ReliaGene, Promega, Applied Biosystems, University of Arizona, Illinois State Police, Orange County CA Coroner, Santa Clara County CA Crime Laboratory, California Department of Justice Sacramento Crime Lab, Marshall University Forensic Science Center, Washington State Patrol Crime Lab in Vancouver, Richland County Sheriff’s DNA and Trace Department, San Diego Sheriff’s Department.

 

APPENDIX 2B. Downloading and uploading from online databases for Y chromosome polymorphisms in human populations.

Database Downloading file format Uploading population data file format DNA-Fingerprint1 p2 ns3 - ns Family Tree DNA4 p  ns - ns SMGF - ns - ns US Y-STR Database - ns - ns Y-Filer Haplotype Database - ns - ns YHRD - ns x5 ns Ysearch6 x ns - ns           1  Some data are deleted from users. 2 p stands for the possibility to download only partial data. 3  ns, non specific; no formally defined format was used. 4  Data from Genographic project may be uploaded.  5  x stands for presence of a specific feature. 6 Accepts everyone’s data, providing a minimum of 8 STR markers (B. Greenspan, personal comunication 02/08/2012).

 

APPENDIX 2C. Matching and other tools available in online databases for Y chromosome polymorphisms in human populations.

Match Database Complete Partial Other population genetics tools DNA-Fingerprint  x1 - - Family Tree DNA - - - SMGF x x - US Y-STR Database x - Mixture analysis tools Y-Filer Haplotype Database x - - YHRD x - AMOVA, Mixture tool Ysearch x x Genetic distances,TMRCA calculator   1 x stands for presence of a specific feature.

 

APPENDIX 2D. Filters in online databases for Y chromosome polymorphisms available in human populations.

Database SNPs HG Reference Ancestry Geographical location Accession number Surname Multiple queries DNA-Fingerprint  x1 x - - x - - x Family Tree DNA - - - - t2 - t - SMGF - - - - - - x - US Y-STR Database - - - x - - - - Y-Filer Haplotype Database - - - - - - - - YHRD x - x - x x - x Ysearch - x - - x - x x                   1 x stands for presence of a specific feature. 2 t stands for reference table.