Sunday, November 30, 2014

Sub Project: Autosomal Pedigree Customization

This is a sub-project for Autosomal Pedigree Creator.

This tool allows to create customized pedigree trees based on different thresholds.

Prerequisites:
Usage:

Copy atree.txt (found in tmp folder after the execution of Autosomal Pedigree Creator) into the root folder of atree2gv and execute the below command from console / command prompt.

atree2gv [-d=<distant-bp-threshold>] [-c=<close-bp-threshold>] [-s=<individual-segment-bp-threshold>] [-g=<large|small>]

E.g.,
atree2gv -d=1000000 -c=1500000000 -s=5000000 -g=large

  • -d=<value>, where value is the threshold in base-pairs for defining distant cousins.
  • -c=<value>, where value is the threshold in base-pairs for defining close relations, usually parent/child. If there are no parent child but only 2nd or third cousins, then you need to enter the value in base-pairs that could be shared by those relations. Parent/child shares 50% of 3.2 billion base pairs. So, the default value is 1500000000.
  • -s=<value>, where value is the threshold in base-pairs for defining individual segments.

Download atree2gv.zip (11.9 MB)

Source Code at GitHub.

License: MIT License.

Sunday, November 23, 2014

Autosomal Pedigree Creator

A tool that automatically creates a pedigree tree based on segment matches from a set of autosomal files. This tool will also let you know how a segment match of an unrelated genetic match is related and through whom. Supports FTDNA, 23andMe and Ancestry files.

Prerequisites:
Usage:
  1. Rename autosomal filenames to have meaningful names like their actual names or Father, Mother etc. No numbers just alphabets.
  2. Copy all the renamed files to a folder.
  3. Browse and select the that folder.
  4. Pedigree created. Enjoy!
Note: To get best results, make sure you have the kit along with the parents’ kits as well. If you don’t have any parents and you got a blank pedigree or you got some individuals omitted, try dump all option.

Screenshots:
Tool in action

Generated Output


Download Autosomal Pedigree Creator.zip (792 KB)

Documentation: Autosomal Pedigree Creator.pdf (1.04 MB) (Online Version)

Source Code at GitHub.

License: MIT License.

Sub Projects: 
FAQ:
Tool hangs at 90%: It means the pedigree is either too large or unable to handle. In this case, just copy the atree.txt result, close the application and use the sub-project Autosomal Pedigree Customization.

Change Log
Version 1.6
  • Hung at 90% bug fixed.
Version 1.5
  • Supports Ancestry files.
Version 1.4
  • Allows alphanumeric names for kits.
Version 1.3
  • Minor bug-fix to provide more accurate pedigree.
Version 1.2
  • Dump-all option for remotely/unrelated autosomal files.
Version 1.1
  • Minor bug-fix.
Version 1.0
  • Initial release.

Related Blogs

Wednesday, November 19, 2014

Ancient Ancestry

Ancient Ancestry is a tool to compare an autosomal DNA with already triangulated ancient DNA segments. The tool will also provide a hierarchical view of how each segment flows through ancients. and allows you to export into an excel friendly format for further analysis. The tool supports FTDNA, 23andMe and Ancestry with build 37 autosomal files.

Prerequisites:
Usage: Open an autosomal file and the tool will automatically plot the matching segments.

Screenshots:




Download Ancient Ancestry.exe (7.66 MB).

Source Code at GitHub.

License: MIT License.

Change Log
Version 1.1
  • 29 Additional Ancient DNA added
  • Incorrect percentage value - bug fixed.
Version 1.0
  • Initial release.

Ancient Hungarian Neolithic genome - NE1

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE1 from Polgár-Ferenci-hát site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and uploaded to GEDmatch as kit# F999937.

Download: 
Reference:
Cristina Gamba, Eppie R. Jones, Matthew D. Teasdale, Russell L. McLaughlin, Gloria Gonzalez-Fortes, Valeria Mattiangeli, László Domboróczki, Ivett Kővári, Ildikó Pap, Alexandra Anders, Alasdair Whittle, János Dani, Pál Raczky, Thomas F. G. Higham, Michael Hofreiter, Daniel G. Bradley & Ron Pinhasi "Genome flux and stasis in a five millennium transect of European prehistory" doi:10.1038/ncomms6257.

Data Used

Saturday, November 15, 2014

Neanderthal Vi33.26 DNA

Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.26 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

Data Used

Neanderthal Vi33.25 DNA

Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.25 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

Data Used

Neanderthal Vi33.16 DNA

Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.16 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs and filtered SNPs are available for download.

Download: 
Reference:
Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

Data Used

Friday, November 14, 2014

Neanderthal Sid1253 DNA

Authors had provided Neanderthal genomes with their publications. I converted the raw data of Sid1253 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

Data Used

Neanderthal Feld1 DNA

Authors had provided Neanderthal genomes with their publications. I converted the raw data of Feld1 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

Data Used

Thursday, November 13, 2014

Kostenki14 Ancient DNA

The origin of contemporary Europeans remains contentious. The authors obtained a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. I converted this raw data of Kostenki 14 into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999936.

Download: 
Reference:
Seguin-Orlando, Andaine, Thorfinn S. Korneliussen, Martin Sikora, Anna-Sapfo Malaspinas, Andrea Manica, Ida Moltke, Anders Albrechtsen et al. "Genomic structure in Europeans dating back at least 36,200 years." Science (2014): aaa0114.

Data Used

Wednesday, November 12, 2014

Ust'-Ishim Ancient DNA

The authors provided a high-quality genome sequence of a 45,000-year-old modern human from Siberia. I converted this raw data of Ust'-Ishim into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999935.

Download: 
Reference:
Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-García, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F. G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich et al. "Genome sequence of a 45,000-year-old modern human from western Siberia" Nature 514, 445–449.

Data Used

Related Blogs


Sunday, November 9, 2014

Ancient Peru NA39 DNA

Samples NA39-50 were obtained from pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD. They were recovered from the site Laguna de los Condores in northeastern Peru. Authors had used bone samples for DNA analysis. I converted the raw data of NA39 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Saturday, November 8, 2014

Ancient Peru NA40 DNA

Samples NA39-50 were obtained from pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD. They were recovered from the site Laguna de los Condores in northeastern Peru. Authors had used bone samples for DNA analysis. I converted the raw data of NA40 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Ancient Peru NA47 DNA

Samples NA39-50 were obtained from pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD. They were recovered from the site Laguna de los Condores in northeastern Peru. Authors had used bone samples for DNA analysis. I converted the raw data of NA47 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Friday, November 7, 2014

Ancient Peru NA50 DNA

Samples NA39-50 were obtained from pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD. They were recovered from the site Laguna de los Condores in northeastern Peru. Authors had used bone samples for DNA analysis. I converted the raw data of NA50 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Ancient Peru NA42 DNA

Samples NA39-50 were obtained from pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD. They were recovered from the site Laguna de los Condores in northeastern Peru. Authors had used bone samples for DNA analysis. I converted the raw data of NA42 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Thursday, November 6, 2014

Ancient Bulgarian T2G2 DNA

Authors had sequenced the DNA from human tooth found in a Thracian tumulus (burial mound) near the village of Stambolovo, Bulgaria. Two small tumuli dating to the Early Iron Age (850-700 BC) were excavated in 2008. A canine tooth from an inhumation burial of a child (c.12 years old) inside a dolium was used for DNA analysis. I converted the raw data of T2G2 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Ancient Bulgaria P192_1 DNA

Authors had sequenced the DNA from human tooth found at the site of a pit sanctuary near Svilengrad, Bulgaria, excavated between 2004 and 2006. The pits are associated with the Thracian culture and date to the Early Iron Age (800-500 BC) based on pottery found in the pits. A total of 67 ritual pits, including 16 pits containing human skele- tons or parts of skeletons, were explored during the excavations. An upper wisdom tooth from an adult male was used for DNA analysis. I converted the raw data of P192_1 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Wednesday, November 5, 2014

Ancient Peru NA41 DNA

Samples NA39-50 were obtained from pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD. They were recovered from the site Laguna de los Condores in northeastern Peru. Authors had used bone samples for DNA analysis. I converted the raw data of NA41 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Gökhem2 Ancient DNA

The authors had generated between 0.01 to 2.2-fold genome wide coverage for 6 neolithic hunter-gathers from pitted ware culture, 4 neolithic farmers from funnel beaker culture and 1 late Mesolithic hunter-gatherer. I converted the raw data of Gökhem2 excavated in Sweden into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999934.

Download: 
Reference:
Skoglund, Pontus, Helena Malmström, Ayça Omrak, Maanasa Raghavan, Cristina Valdiosera, Torsten Günther, Per Hall et al. "Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers." Science 344, no. 6185 (2014): 747-750.

Data Used

Tuesday, November 4, 2014

PhyloTreeMT AddOn for Google Chrome

PhyloTree MT AddOn is a chrome browser extension that adds additional functionality of plotting your mt-DNA mutations on mtDNA PhyloTree (www.phylotree.org/tree/main.htm).

The extension adds a number of features to mtDNA PhyloTree based on your mt-DNA Results:

  • Allows upto 10 kits.
  • Highlights your mutations in mtDNA PhyloTree.

Note: To use this add-on, you must have purchased a mt-DNA test from any of the DNA testing companies for genealogy purposes and had received the results as RSRS. PhyloTree MT is from www.phylotree.org/tree/main.htm. Once the AddOn is installed, go to the Options and enter your mt-DNA mutations.

Prerequisites: Google Chrome

Screenshot:


PhyloTree AddOn Plotting.


Usage: Install the addon and go to Options page and enter your mt-Mutations. Then, to go www.phylotree.org/tree/main.htm to get those entered mutations plotted.

Install: PhyloTreeMT AddOn

Source Code at GitHub.

Change Log: 1.0.1

  • Doesn't plot back mutations and mutations in brackets - fixed.

Change Log :1.0.0
  • Initial Release.

Monday, November 3, 2014

Australian Aboriginal DNA

The authors presented an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. The nuclear genome was sequenced to an overall depth of 6.4-fold. It had a high degree of fragmentation, but no genotype level evidence of sample contamination by DNA from sample handlers of European descent was detected. I converted this genome into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch.

Download: 
Reference:
Rasmussen, M; Guo, X; Wang, Y; Lohmueller, KE; Rasmussen, S; Albrechtsen, A; Skotte, L; Lindgreen, S; Metspalu, M; Jombart, T; Kivisild, T; Zhai, W; Eriksson, A; Manica, A; Orlando, L; De La Vega, FM; Tridico, S; Metspalu, E; Nielsen, K; Avila-Arcos, MC; Moreno-Mayar, JV; Muller, C; Dortch, J; Gilbert, MT; Lund, O; Wesolowska, A; Karmin, M; Weinert, LA; Wang, B; Li, J; Tai, S; Xiao, F; Hanihara, T; van Driem, G; Jha, AR; Ricaut, FX; de Knijff, P; Migliano, AB; Romero, IG; Kristiansen, K; Lambert, DM; Brunak, S; Forster, P; Brinkmann, B; Nehlich, O; Bunce, M; Richards, M; Gupta, R; Bustamante, CD; Krogh, A; Foley, RA; Lahr, MM; Balloux, F; Sicheritz-Ponten, T; Villems, R; Nielsen, R; Wang, J; Willerslev, E; (2011): Genomic sequence from an Aboriginal Australian; GigaScience. http://dx.doi.org/10.5524/100010

Data Used

Ancient Hungarian genome - Bronze Age - BR2

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of BR2 from Ludas-Varjú-dűlő site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999933.

Download: 
Reference:
Cristina Gamba, Eppie R. Jones, Matthew D. Teasdale, Russell L. McLaughlin, Gloria Gonzalez-Fortes, Valeria Mattiangeli, László Domboróczki, Ivett Kővári, Ildikó Pap, Alexandra Anders, Alasdair Whittle, János Dani, Pál Raczky, Thomas F. G. Higham, Michael Hofreiter, Daniel G. Bradley & Ron Pinhasi "Genome flux and stasis in a five millennium transect of European prehistory" doi:10.1038/ncomms6257.

Data Used

Related Blogs

Sunday, November 2, 2014

Ancient Hungarian Neolithic genome - NE6

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE6 from Apc-Berekalja I. site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999932.

Download: 
Reference:
Cristina Gamba, Eppie R. Jones, Matthew D. Teasdale, Russell L. McLaughlin, Gloria Gonzalez-Fortes, Valeria Mattiangeli, László Domboróczki, Ivett Kővári, Ildikó Pap, Alexandra Anders, Alasdair Whittle, János Dani, Pál Raczky, Thomas F. G. Higham, Michael Hofreiter, Daniel G. Bradley & Ron Pinhasi "Genome flux and stasis in a five millennium transect of European prehistory" doi:10.1038/ncomms6257.

Data Used
Related Blogs

Saturday, November 1, 2014

Ancient Peru NA43 DNA

Samples NA39-50 were obtained from pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD. They were recovered from the site Laguna de los Condores in northeastern Peru. Authors had used bone samples for DNA analysis. I converted the raw data of NA43 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used

Ancient Bulgaria K8 DNA

Authors had sequenced the DNA from human tooth found in the Yakimova Mogila Tumulus, which dates to the Iron Age (450-400 BC), near Krushare, Bulgaria. An aristocratic inhumation burial containing rich grave goods was excavated in 2008. A molar from one individual, probably male, was used for DNA analysis. I converted the raw data of this K8 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs and the filtered SNPs are available for download.

Download: 
Reference:
Carpenter, Meredith L., Jason D. Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen et al. "Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries." The American Journal of Human Genetics 93, no. 5 (2013): 852-864.

Data Used