Análisis genético del individuo de Chan do Lindeirocaracterización de su mitogenoma y situación de la muestra en el contexto paleogenético europeo.

Referencias bibliográficas

• Bramanti, B., Thomas, M.G., Haak, W., Unterlaender, M., Jores, P., Tambets, K., Atan-Aitis-Jacobs, L., Haidle, M.N., Jankauskas, R., Kind, C.J., et al. 2009. Genetic discontinuity between local hunter-gatherers and central Europe's first farmers. Science 326, 137-140.
• Briggs, A.W., Stenzel, U., Johnson, P.L., Green, R.E., Kelso, J., Prufer, K., Meyer, M., Krause, J., Ronan, M.T., Lachmann, M. y Pääbo, S. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. USA 104, 14616-14621.
• Fu, Q., Mittnik, A., Johnson, P.L., Bos, K., Lari, M., Bollongino, R., Sun, C., Giemsch, L., Schmitz, R., Burger, J., et al. 2013. A revised timescale for human evolution based on ancient mitocondrial genomes. Curr. Biol. 23, 553-559.
• Fu, Q., Hajdinjak, M., Moldovan, O.T., Constantin, S., Malltck, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, L., Nickel, B., et al. 2015. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216-219.
• Gamba, C., Jones, E.R., Teasdale, M.D., Mclaughlin, R.L., González-Fortes, G., Mattiangeli, V., Domboróczkt, L., Kövári, I., Pap, I., Anders, A., Whittle, A., Dani, J., Raczky, P., Higham, T.F., Hofreiter, M., Bradley, D.G., Y Pinhasi, R. 2014. Genome flux and stasis in a five millennium transect of European prehistory. Nature Commun. 5, 5257.
• Ginolhac, A., Rasmussen, M., Gilbert, M.T. et al (2011) mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 27(15), 2153-2155.
• Günther, T., Valdiosera, C., Malmström, H. et al. 2015. Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. Proc. Natl. Acad. Sci. USA 1 12(38), 11917-11922.
• Haak, W., Lazaridis, L., Patterson, N. et al. 2015. Massive migration from the steppe was a source for Indo­-European languages in Europe. Nature 522, 207.
• Hodges, E., Rooks, M., Xuan, Z., et al. 2009. Hybrid selection of discrete genomic intervals on custom-designed rnicroarrays for massively parallel sequencing. Nature Protocols 4, 960-974.
• Jones, E.R., González-Fortes, G., Connell, S. et al 2015. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature Commun. 6, 8912. DOI: https://doi.org/10.1038/ncornrns99
• Kettunen, J., Silander, K., Saarela, O., et al 2010. European lactase persistence genotype shows evidence of association with increase in body mass index. Hum. Mol. Genet. 19(6), 1129-1136.
• Krause, J., Briggs, A.W., Kircher, M., Maricic, T., Zwyns, N., Derevianko, A., Pääbo, S. 2010. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr. Biol. 20, 231-236.
• Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P.H., Schraiber, J.G., Castellano, S., Lipson, M., et al. 2014. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409-413.
• Lazaridis, I., Nadel, D., Rollefson, G. et al 2016. The genetic structure of the world’s first farmers. Nature 536, 419-424.
• Li, H., Durbin, R. 2009. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25, 1754-1760.
• Malyarchuk, B., Derenko, M., Grzybowski, T., Perkova, M., Rogalla, U., Vanecek, T. Tsybovsky, I. 2010. The peopling of Europe from the mitochondrial haplogroup U5 perspective. PLoS One 5(4), e10285.
• Maricic, T., Whitten, M., Pääbo, S. 2010. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 5(11), e14004.
• Martin, M. 2011. Cutadapt removes adapter sequences from high throughput sequencing reads. EMBnet.journal 17(1), 10-11.
• Mathieson I., Lazaridis I., Rohland N. et al. 2015. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499-503.
• Mckenna, A., Hanna, M., Banks, E., et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.
• Meyer, M., Kircher, M. 2010. Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing. Cold Spring Harb. Pro- toc. doi: https://doi.org/10.1101/pdb.prot5448.
• Milne, I., Stephen, G., Bayer, M., et al. 2013. Using Tablet for visual exploration of secondgeneration sequencing data. Briefings in Bioinformatics 14(2), 193-202.
• Olalde, I., Allentoft, M.E., Sanchez-Quinto, F. 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. 2014. Nature 507(7491), 225-228.
• Olalde, I., Schroeder, H., Sandoval-Velasco, M. et al. 2015. A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures. Mol. Biol. Evol. 32(12), 3132-3142.
• Orlando, L., Ginolhac, A., Raghavan, M., Vilstrup, J., Rasmussen, M., Magnussen, K., Steinmann, K.E., Kapranov, P., Thompson, J.F., Zazula, G., et al. 2011. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res. 21, 1705-1719.
• Pala, M., Achilli, A., Olivieri, A., Kashani, B., Perego, U., et al. 2009. Mitochondrial haplogroup U5b3: A distant echo of the Epipaleolithic in Italy and the legacy of the early Sardinians. Am. J. Hum. Genet. 84, 814-821.
• Pinhasi, R., Thomas, M.G., Hofreiter, M., Currat, M., Burger, J. 2012. The genetic history of Europeans. Trends Genet. 28(10), 496-505.
• Pneuman, A., Budimlija, Z.M., Caragine, T., et al. 2012. Verification of eye and skin color predictors in various populations. Leg. Med. 14, 78-83.
• Posth, C., Renaud, G., Mittnik, A. et al 2016. Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe. Current Biology 26, 827-833.
• Rohland, N., Siedel, H., Hofreiter, M. 2010. A rapid column-based ancient DNA extraction method for increased sample throughput. Mol. Ecol. Resour. 10(4), 677-683.
• Sanchez-Quinto, F., Schroeder, H., Ramirez, O. et al. 2012. Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Current Biology 22, 1494-1499.
• Spichenok, O., Budimlija, Z.M., Mitchell, A.A., et al. 2011. Prediction of eye and skin color in diverse populations using seven SNPs. Forensic Sci. Int. Genet. 5, 472-478.
• Stamatakis, A. 2014. RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 30(9), 1312-1323.
• Tambets, K., Rootsi, S., Kivisild, T., Help, H., Serk, P., Loogvali, E.L., Tolk, H.V., Reidla, M., Metspalu, E., Pliss, L., et al. 2004. The western and eastern roots of the Saami. the story of genetic ‘‘outliers’’ told by mitochondrial DNA and Y chromosomes. Am. J. Hum. Genet. 74, 661-682.
• Thorvaldsdóttir, H., Robinson, J.T., Mesirov, J.P. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14, 178-192.
• Walsh, S., Liu, F., Wollstein, A. et al. 2013. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci. Int. Genet. 7, 98-115.
• Ye, K., Gu, Z. 2011. Recent advances in understanding the role of nutrition in human genome evolution. Adv. Nutr. 2(6), 486-496.