DOI: 10.5061/dryad.4xgxd25nx
title: Ancient genomes from eastern Kazakhstan reveal dynamic genetic legacy of Inner Eurasian hunter-gatherers

description: Eurasian Steppe meets the mountain forests of Inner Asia. Here we report
 genome-wide data of two Early Neolithic (EN) hunter-gatherers and 19
 Middle-Late Bronze Age (MLBA) pastoralists, from the site of Koken in the
 Upper Irtysh River region in eastern Kazakhstan. We find that the two EN
 individuals differed in their genetic profiles and yet were second-degree
 relatives. They were genetically most similar to subsequent Neolithic
 individuals in the Irtysh region, while contemporaneous hunter-gatherers
 from the Tobol-Ishim and Upper Ob River regions had distinct genetic
 profiles, likely influenced by riverine geography. The Koken MLBA
 individuals were genetically similar to other MLBA steppe pastoralists,
 while genetic outliers provide evidence of two distinct trajectories of
 admixture with local hunter-gatherer populations. These findings
 illuminate the dynamic population structure of Inner Asian
 hunter-gatherers and their genetic legacy in subsequent pastoralist
 populations.
description: # Ancient genomes from eastern Kazakhstan reveal dynamic genetic legacy of
 Inner Eurasian hunter-gatherers Dataset DOI:
 [10.5061/dryad.4xgxd25nx](10.5061/dryad.4xgxd25nx) ## Description of the
 data and file structure This repository contains genotype data and scripts
 used for the analyses in "Ancient genomes from eastern Kazakhstan
 reveal dynamic genetic legacy of Inner Eurasian hunter-gatherers".
 ### Files and variables #### File: Koken_Supplementary_Figure_12_PCA.eval
 **Description:** This file contains the eigenvalues from the PCA performed
 using present-day western Eurasian individuals (see Supplementary Figure
 11, 12 and 14). #### File: Koken_Figure_2_map_Lat_Lon_coordinates.csv
 **Description:** This file contains the meta data used for plotting the
 map in Figure 2 (see Figure 2). ##### Variables * Study Group: Population
 ID  * Latitude: Latitude of the excavated site  * Longitude: Longitude of
 the excavated site  * Age average: Average radiocarbon date of the
 excavated human remains (i.e., the estimated time period when the
 individuals lived, not their age at death) * pch: pch parameter used to
 represent this population in R plots * color: col or bg parameter used to
 represent this population in R plots * IID: Individual ID #### File:
 Koken_Figure_2_PCA.evec.txt.gz **Description:** This file contains
 eigenvectors from the PCA performed using present-day Eurasian (see Figure
 2, Supplementary Figure 11 and 14). #### File:
 Koken_Figure_2_Radiocarbon_dates.csv **Description:** This file contains
 the meta data used for plotting the map in Figure 2 (see Figure 2). #####
 Variables * Study Group: Population ID  * Order: The order in which
 populations should be added (e.g., to plots) in R * Latitude: Latitude of
 the excavated site  * Longitude: Longitude of the excavated site  * Dates:
 Average radiocarbon date of the excavated human remains * pch: pch
 parameter used to represent this population in R plots * color: col or bg
 parameter used to represent this population in R plots * IID: Individual
 ID #### File: Koken_ancients_21.ind **Description:** `ind` file in
 EIGENSTRAT format for the 21 individuals from the Koken site. #### File:
 Koken_Figure_2_PCA.eval **Description:** This file contains eigenvalues
 from the PCA performed using present-day Eurasian (see Figure 2,
 Supplementary Figure 11 and 14). #### File: Koken_Figure_2_PCA.evec
 **Description:** This file contains eigenvectors from the PCA performed
 using present-day Eurasian (see Figure 2, Supplementary Figure 11 and 14).
 #### File: Koken_Supplementary_Figure_12_PCA.evec.txt.gz
 **Description:** This file contains the eigenvectors from the PCA
 performed using present-day western Eurasian individuals (see
 Supplementary Figure 11, 12 and 14). #### File:
 Koken_Supplementary_Figure_12_PCA.evec **Description:** This file contains
 the eigenvectors from the PCA performed using present-day western Eurasian
 individuals (see Supplementary Figure 11, 12 and 14). #### File:
 Koken_ancients_21.snp **Description:** `snp` file in EIGENSTRAT format for
 the 21 individuals from the Koken site. #### File: Koken_ancients_21.geno
 **Description:** `geno` file in EIGENSTRAT format for the 21 individuals
 from the Koken site. #### File:
 Supplementary_Figure_15_DATES_Koken_MLBA_o2.Krasnoyarsk_MLBA_Irtysh_UpperOb_HG.txt **Description:** Results from the DATES program modeling *Koken_MLBA_o2* as an admixture between *Krasnoyarsk_MLBA* and *Irtysh_UpperOb_HG* (see Figure 4 and Supplementary Figure 15). #### File: Supplementary_Figure_15_DATES_Zevakinskiy_LBA.Krasnoyarsk_MLBA_Irtysh_UpperOb_HG.txt **Description:** Results from the DATES program modeling *Zevakinskiy_LBA* as an admixture between *Krasnoyarsk_MLBA* and *Irtysh_UpperOb_HG* (see Figure 4 and Supplementary Figure 15). #### File: Supplementary_Figure_15_DATES_Koken_MLBA_o1.Krasnoyarsk_MLBA_Irtysh_UpperOb_HG.txt **Description:** Results from the DATES program modeling *Koken_MLBA_o1 *as an admixture between *Krasnoyarsk_MLBA* and *Irtysh_UpperOb_HG* (see Figure 4 and Supplementary Figure 15). #### File: Supplementary_Figure_15_DATES_Koken_MLBA.Sintashta_MLBA_Irtysh_UpperOb_HG.txt **Description:** Results from the DATES program modeling *Koken_MLBA *as an admixture between *Sintashta_MLBA* and *Irtysh_UpperOb_HG* (see Figure 4 and Supplementary Figure 15). #### File: Supplementary_Figure_15_DATES_Krasnoyarsk_MLBA.Sintashta_MLBA_Irtysh_UpperOb_HG.txt **Description:** Results from the DATES program modeling *Krasnoyarsk_MLBA *as an admixture between *Sintashta_MLBA* and *Irtysh_UpperOb_HG* (see Figure 4 and Supplementary Figure 15). #### File: Koken_Supplementary_Figure_8_hapROH.csv **Description:** Results from the hapROH program detecting runs of homozygosity (ROH) blocks (see Supplementary Figure 8). #### File: Koken_Supplementary_Figure_7_pedsim_simulated_IBD.txt **Description:** Results from the pedsim program simulating IBD segments for specified kinship relationships (see Supplementary Figure 7). #### File: DataProcessing_MPI_batch17_script_250225_TF1-2.txt **Description:** The script used for processing raw sequencing data from initial quality control to alignment and filtering. #### File: Koken_EN_2_imputation_250228.txt **Description:** The script used to run GLIMPSE2 to impute 2 Koken EN individuals. #### File: Koken_EN_run_ancIBD_250304.txt **Description:** The script used to run ancIBD program between Koken_EN1 and Koken_EN2. #### File: run_ancIBD_to_detect_IBD2_241228.txt **Description:** The script used to detect IBD2 between Koken_EN1 and Koken_EN2. #### File: Koken_MLBA_PMR_script_250508.txt **Description:** The script used to calculate pairwise mismatch rates (PMR) to investigate kinship among Koken individuals. #### File: Koken_Supplementary_Figure_7_compare_ancIBD_pedsim.zip **Description:** The script and input file used to run pedsim to investigate the potential kinship between two Koken Early Neolithic individuals (see Supplementary Figure 7) #### File: Koken_MLBA_qpAdm_script_250522.txt **Description:** The script used to run qpAdm to investigate the admixture sources and proportions of the newly sequenced Koken MLBA individuals (see Figure 4). #### File: Koken_EN_qpAdm_OGs_script_250512.txt **Description:** The script used to run qpAdm to investigate the genetic profiles of the newly sequenced Koken EN individuals (see Figure 3 and Supplementary Figure 13). #### File: Koken_EN_qpAdm_script_241226.txt **Description:** The script used to run qpAdm to investigate the genetic profiles of the newly sequenced Koken EN individuals (see Figure 3). #### File: Koken_f3_f4_PCA_script_250305.txt **Description:** The script used to run PCA, f3-, and f4-statistics to investigate the genetic profiles of the newly sequenced Koken individuals (see Figure 2, Supplementary Figure 9-12 and 14). #### File: Koken_DATES_script_250425.txt **Description:** The script used to run the DATES program for estimating admixture dates (see Figure 4 and Supplementary Figure 15). #### File: Koken_DATES_script_250425_2.txt **Description:** The script used to run the DATES program for estimating admixture dates (see Figure 4 and Supplementary Figure 15). ## Access information Other publicly accessible location of the data: [https://github.com/CWJeongLab/Koken](https://github.com/CWJeongLab/Koken)