Dataset Information

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

ABSTRACT: There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

SUBMITTER: Nakatsuka N

PROVIDER: S-EPMC7304944 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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A Paleogenomic Reconstruction of the Deep Population History of the Andes.

Nakatsuka Nathan N Lazaridis Iosif I Barbieri Chiara C Skoglund Pontus P Rohland Nadin N Mallick Swapan S Posth Cosimo C Harkins-Kinkaid Kelly K Ferry Matthew M Harney Éadaoin É Michel Megan M Stewardson Kristin K Novak-Forst Jannine J Capriles José M JM Durruty Marta Alfonso MA Álvarez Karina Aranda KA Beresford-Jones David D Burger Richard R Cadwallader Lauren L Fujita Ricardo R Isla Johny J Lau George G Aguirre Carlos Lémuz CL LeBlanc Steven S Maldonado Sergio Calla SC Meddens Frank F Messineo Pablo G PG Culleton Brendan J BJ Harper Thomas K TK Quilter Jeffrey J Politis Gustavo G Rademaker Kurt K Reindel Markus M Rivera Mario M Salazar Lucy L Sandoval José R JR Santoro Calogero M CM Scheifler Nahuel N Standen Vivien V Barreto Maria Ines MI Espinoza Isabel Flores IF Tomasto-Cagigao Elsa E Valverde Guido G Kennett Douglas J DJ Cooper Alan A Krause Johannes J Haak Wolfgang W Llamas Bastien B Reich David D Fehren-Schmitz Lars L

Cell 20200507 5

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Hig ...[more]

PMID: 32386546

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Project description:BackgroundThe advancements in DNA sequencing technologies have allowed researchers to progress from the analyses of a single organism towards the deep sequencing of a sample of organisms. With sufficient sequencing depth, it is now possible to detect subtle variations between members of the same species, or between mixed species with shared biomarkers, such as the 16S rRNA gene. However, traditional sequencing analyses of samples from largely homogeneous populations are often still based on multiple sequence alignments (MSA), where each sequence is placed along a separate row and similarities between aligned bases can be followed down each column. While this visual format is intuitive for a small set of aligned sequences, the representation quickly becomes cumbersome as sequencing depths cover loci hundreds or thousands of reads deep.FindingsWe have developed ANDES, a software library and a suite of applications, written in Perl and R, for the statistical ANalyses of DEep Sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA). Tools include the root mean square deviation (RMSD) plot, which allows for the visual comparison of multiple samples on a position-by-position basis, and the computation of base conversion frequencies (transition/transversion rates), variation (Shannon entropy), inter-sample clustering and visualization (dendrogram and multidimensional scaling (MDS) plot), threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values.ConclusionsAs new sequencing technologies evolve, deep sequencing will become increasingly cost-efficient and the inter and intra-sample comparisons of largely homogeneous sequences will become more common. We have provided a software package and demonstrated its application on various empirically-derived datasets. Investigators may download the software from Sourceforge at https://sourceforge.net/projects/andestools.

Dataset Information

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

Publications

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

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