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Ancient DNA sequencing of a Middle Woodland variant: a … · 2016-09-29 · Ancient DNA sequencing...
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Ancient DNA sequencing of a Middle Woodland variant: a discussion of the Ray Site Elizabeth A. Nelson 1 , Jane E. Buikstra 2 , and John V. Planz 3 1 Department of Integrative Physiology and Anatomy, University of North Texas Health Science Center, 2 Center for Bioarchaeological Research, Arizona State University, 3 Department of Molecular and Medical Genetics, University of North Texas Health Science Center The Ray Site Hypotheses Materials and Methods 1. Dulik, M. C., Zhadanov, S. I., Osipova, L. P., Askapuli, A., Gau, L., Gokcumen, O. & Schurr, T. G. (2012). Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians. The American Journal of Human Genetics, 90(2), 229-246. 2. Flotow 3. Karafet et al, Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes. (pdf) American Journal of Human Genetics, 69:615-628, 2001. 4. Kidd KK, Kidd JR, Speed WC, Fang R, Furtado MR, Hyland FC, Pakstis AJ. "Expanding data and resources for forensic use of SNPs in individual identification.". Forensic Sci Int Genet. 6:646-52. (2012) 5. Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A , Maiers M, Middha M, Friedlaender FR, Kidd JR. "Progress toward an efficient panel of SNPs for ancestry inference". Forensic Sci Int Genet. 23-32. (2014) 6. Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, Seldin MF. "Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America". Hum Mutat 30:69-78. (2009) 7. Hammer et al, Hierarchical Patterns of Global Human Y-Chromosome Diversity. Molecular Biology and Evolution, 18:1189-1203, 2001. 8. Hammer, M. F., Chamberlain, V. F., Kearney, V. F., Stover, D., Zhang, G., Karafet, T., ... & Redd, A. J. (2006). Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases. Forensic science international, 164(1), 45-55. 9. Nievergelt CM, Maihofer AX,Shekhtman T,Libiger O,Wang X,Kidd KK and Kidd JR "Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel". Investigative Genetics (Epub) 4:13. (2013) 10. MYcroarray (2013) MYbaits Manual. Available at www.mycroarray.com/pdf/ MYbaits-manual.pdf. Accessed March 1, 2014. 11. Pakstis AJ, Speed WC, Fang R, Hyland FCL, Furtado MR, Kidd JR, Kidd KK. "SNPs for a universal individual identification panel". Human Genetics 127:315-24. (2010) 12. Reich, D., Patterson, N., Campbell, D., Tandon, A., Mazieres, S., Ray, N., ... & Barrantes, R. (2012). Reconstructing native American population history. Nature, 488(7411), 370-374. References Genetic analysis of the Ray site will allow us to test the following hypotheses: 1. The Ray site was an accretional cemetery used by groups from various locales. 2. The Ray site was an isolated bluff top community, having little external interaction. Although variation in burial pattern and artifact distribution suggest the Ray site may have been used by multiple groups, this hypothesis has not been tested with other lines of evidence. Identification of genetic relationships within the Ray site will provide a greater understanding of burial organization and community composition. Furthermore, the information gained through genetic analysis of the Ray site community allows for the investigation of interpopulation genetic relationships with contemporaneous sites. Through such analyses we may be able to observe evidence of mutli-group interaction or find support for the hypothesis of the Ray site as an isolate. The Ray site (Br 104) is located in western Illinois on a steep, narrow ridge near the confluence of the Illinois and La Moine rivers (Figure 1 and 2) 2 . It is a Middle Woodland burial site estimated to be in use from 50 BC – AD 450. The inventory of the Ray site burials records a minimum number of 117 individuals. The Ray site varies from its contemporaries in numerous ways 2 : • Cemetery is not mounded • No evidence of a superstructure characteristic of Middle Woodland sites • Burials were interred in a linear pattern, with 4 clusters • Burials of isolated elements • There is an isolated concentration of 9 burials in the southeast area of the site • The directional orientation of interred individuals varies within the site • Remains are found in both extended and flexed positions (Figure 3). For this pilot project we identified six individuals from different areas of the site and selected a tooth from each for genetic analysis. (Figure 4). Comprehensive genetic analysis will include mining the genome while also targeting individual identity markers (IISNP). This panel includes autosomal SNPs and paternal and specific sequences of DNA using a custom liquid-phase DNA capture system from Mycroarray (Figure 5). We have created a custom library of 600 single nucleotide polymorphisms (SNP) including ancestry informative markers (AIM) and maternal markers (Table 1). Through this analysis we will be able to identify: • Geneflow • Admixture • Biological relationships Source Number and Type Citations ISOGG Y-DNA SNP Index - As provided on ISOGG 44 Y-SNPs 1, 3, 7, 8 Kidd Lab - As provided on ALFRED 55 AISNPs 5 Kidd Lab - As provided on ALFRED 44 AISNPs - Kenneth K. Kidd et al. "Data unpublished". Kidd Lab - As provided on ALFRED 86 IISNPs 4, 11 Nievergelt’s List - As provided on ALFRED 41 AISNPs 9 Reich Lab 447 12 Seldin’s List -as provided on ALFRED 128 AISNPs 6 Extraction of genetic material and enrichment is taking place at the Center for Human Identification University of North Texas Health Science Center. The information this analysis yields will lead not only to a greater understanding of the Ray Site population in terms of biological relationships and genetic background of the site but will also offer insight into the peopling of North America. We plan further sampling and testing of the Ray site remains, as well as complimentary chemical analysis to enhance studies on migration. We would like to thank Jason King, Director of Research for the Center for American Archeology, for allowing access to the collection and providing work space. A very heartfelt thank you to Dr. Claire Kirchhoff for her advice with the development of this project and poster. Thanks so much to Dr. Laura Gaydosh Combs for many hours in and out of the laboratory. Thank you to Chris Shelton, Archaeologist Project Manager SWCA, for creating maps. Thank you to Dr. David Reich of Harvard for making previously collected data available. Thank you to Dr. Kenneth Kidd for the development of ALFRED and availability of genetic data. A very big thank you to UNTHSC for accessibility to materials and facilities for collection of samples and processing and analysis of genetic materials. Thank you to our friends and family for support during this project. A very special thank you to Isaac Weston, the coolest kid I know. Acknowledgements Figure 4. Ray 3-19, mandible, occlusal view. Table 1. List of sources for custom SNP bait panel. Figure 5. Illustrating process from Mycroarray of baiting, capturing, and sequencing. Figure 1. Location of the Ray site, west Illinois 2 . Figure 2. Map of the Ray site burials. Individuals sampled for Genetic testing circled in red 2 . Figure 2. Map of approximate location of the Ray site. *Redundant SNPs were removed from final SNP collection for custom bait panel.
Transcript of Ancient DNA sequencing of a Middle Woodland variant: a … · 2016-09-29 · Ancient DNA sequencing...
Ancient DNA sequencing of a Middle Woodland variant: a discussion of the Ray Site
Elizabeth A. Nelson1, Jane E. Buikstra2, and John V. Planz3 1Department of Integrative Physiology and Anatomy, University of North Texas Health Science Center, 2 Center for
Bioarchaeological Research, Arizona State University, 3Department of Molecular and Medical Genetics, University of North Texas Health Science Center
The Ray Site
Hypotheses
Materials and Methods
1. Dulik, M. C., Zhadanov, S. I., Osipova, L. P., Askapuli, A., Gau, L., Gokcumen, O. & Schurr, T. G. (2012). Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians. The American Journal of Human Genetics, 90(2), 229-246.
2. Flotow 3. Karafet et al, Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes. (pdf) American Journal of Human Genetics, 69:615-628, 2001. 4. Kidd KK, Kidd JR, Speed WC, Fang R, Furtado MR, Hyland FC, Pakstis AJ. "Expanding data and resources for forensic use of SNPs in individual identification.". Forensic Sci Int
Genet. 6:646-52. (2012) 5. Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A , Maiers M, Middha M, Friedlaender FR, Kidd JR. "Progress toward an efficient panel of SNPs for ancestry
inference". Forensic Sci Int Genet. 23-32. (2014) 6. Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, Seldin MF. "Ancestry informative marker
sets for determining continental origin and admixture proportions in common populations in America". Hum Mutat 30:69-78. (2009) 7. Hammer et al, Hierarchical Patterns of Global Human Y-Chromosome Diversity. Molecular Biology and Evolution, 18:1189-1203, 2001. 8. Hammer, M. F., Chamberlain, V. F., Kearney, V. F., Stover, D., Zhang, G., Karafet, T., ... & Redd, A. J. (2006). Population structure of Y chromosome SNP haplogroups in the
United States and forensic implications for constructing Y chromosome STR databases. Forensic science international, 164(1), 45-55. 9. Nievergelt CM, Maihofer AX,Shekhtman T,Libiger O,Wang X,Kidd KK and Kidd JR "Inference of human continental origin and admixture proportions using a highly discriminative ancestry
informative 41-SNP panel". Investigative Genetics (Epub) 4:13. (2013) 10. MYcroarray (2013) MYbaits Manual. Available at www.mycroarray.com/pdf/ MYbaits-manual.pdf. Accessed March 1, 2014. 11. Pakstis AJ, Speed WC, Fang R, Hyland FCL, Furtado MR, Kidd JR, Kidd KK. "SNPs for a universal individual identification panel". Human Genetics 127:315-24. (2010) 12. Reich, D., Patterson, N., Campbell, D., Tandon, A., Mazieres, S., Ray, N., ... & Barrantes, R. (2012). Reconstructing native American population history. Nature, 488(7411), 370-374.
References
Genetic analysis of the Ray site will allow us to test the following hypotheses: 1. The Ray site was an accretional
cemetery used by groups from various locales.
2. The Ray site was an isolated bluff top
community, having little external interaction.
Although variation in burial pattern and artifact distribution suggest the Ray site may have been used by multiple groups, this hypothesis has not been tested with other lines of evidence. Identification of genetic relationships within the Ray site will provide a greater understanding of burial organization and community composition. Furthermore, the information gained through genetic analysis of the Ray site community allows for the investigation of interpopulation genetic relationships with contemporaneous sites. Through such analyses we may be able to observe evidence of mutli-group interaction or find support for the hypothesis of the Ray site as an isolate.
The Ray site (Br 104) is located in western Illinois on a steep, narrow ridge near the confluence of the Illinois and La Moine rivers (Figure 1 and 2)2. It is a Middle Woodland burial site estimated to be in use from 50BC – AD450. The inventory of the Ray site burials records a minimum number of 117 individuals. The Ray site varies from its contemporaries in numerous ways2: • Cemetery is not mounded • No evidence of a superstructure
characteristic of Middle Woodland sites • Burials were interred in a linear pattern,
with 4 clusters • Burials of isolated elements • There is an isolated concentration of 9
burials in the southeast area of the site • The directional orientation of interred
individuals varies within the site • Remains are found in both extended and
flexed positions (Figure 3).
For this pilot project we identified six individuals from different areas of the site and selected a tooth from each for genetic analysis. (Figure 4). Comprehensive genetic analysis will include mining the genome while also targeting individual identity markers (IISNP). This panel includes autosomal SNPs and paternal and specific sequences of DNA using a custom liquid-phase DNA capture system from Mycroarray (Figure 5). We have created a custom library of 600 single nucleotide polymorphisms (SNP) including ancestry informative markers (AIM) and maternal markers (Table 1). Through this analysis we will be able to identify: • Geneflow • Admixture • Biological relationships
Source Number and Type Citations ISOGG Y-DNA SNP Index - As provided on ISOGG
44 Y-SNPs 1, 3, 7, 8
Kidd Lab - As provided on ALFRED
55 AISNPs 5
Kidd Lab - As provided on ALFRED
44 AISNPs - Kenneth K. Kidd et al. "Data unpublished".
Kidd Lab - As provided on ALFRED
86 IISNPs 4, 11
Nievergelt’s List - As provided on ALFRED
41 AISNPs 9
Reich Lab 447 12
Seldin’s List -as provided on ALFRED
128 AISNPs 6
Extraction of genetic material and enrichment is taking place at the Center for Human Identification University of North Texas Health Science Center. The information this analysis yields will lead not only to a greater understanding of the Ray Site population in terms of biological relationships and genetic background of the site but will also offer insight into the peopling of North America. We plan further sampling and testing of the Ray site remains, as well as complimentary chemical analysis to enhance studies on migration.
We would like to thank Jason King, Director of Research for the Center for American Archeology, for allowing access to the collection and providing work space. A very heartfelt thank you to Dr. Claire Kirchhoff for her advice with the development of this project and poster. Thanks so much to Dr. Laura Gaydosh Combs for many hours in and out of the laboratory. Thank you to Chris Shelton, Archaeologist Project Manager SWCA, for creating maps. Thank you to Dr. David Reich of Harvard for making previously collected data available. Thank you to Dr. Kenneth Kidd for the development of ALFRED and availability of genetic data. A very big thank you to UNTHSC for accessibility to materials and facilities for collection of samples and processing and analysis of genetic materials. Thank you to our friends and family for support during this project. A very special thank you to Isaac Weston, the coolest kid I know.
Acknowledgements
Figure 4. Ray 3-19, mandible, occlusal view.
Table 1. List of sources for custom SNP bait panel.
Figure 5. Illustrating process from Mycroarray of baiting, capturing, and sequencing.
Figure 1. Location of the Ray site, west Illinois2.
Figure 2. Map of the Ray site burials. Individuals sampled for Genetic testing circled in red2.
Figure 2. Map of approximate location of the Ray site.
*Redundant SNPs were removed from final SNP collection for custom bait panel.
