Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India

Harney, Éadaoin; Nayak, Ayushi; Patterson, Nick; Joglekar, Pramod; Mushrif-Tripathy, Veena; Mallick, Swapan; Rohland, Nadin; Sedig, Jakob; Adamski, Nicole; Bernardos, Rebecca; Broomandkhoshbacht, Nasreen; Culleton, Brendan J.; Ferry, Matthew; Harper, Thomas K.; Michel, Megan; Oppenheimer, Jonas; Stewardson, Kristin; Zhang, Zhao; Harashawaradhana,; Bartwal, Maanwendra Singh; Kumar, Sachin; Diyundi, Subhash Chandra; Roberts, Patrick; Boivin, Nicole; Kennett, Douglas J.; Thangaraj, Kumarasamy; Reich, David; Rai, Niraj

doi:10.1038/s41467-019-11357-9

Cited by 21 publications

(8 citation statements)

References 74 publications

(59 reference statements)

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“…A prime example of this is Roopkund Lake -a Himalayan site where hundreds of skeletal remains of unknown provenance have been found at over 5,000 meters above sea level. Harney et al 54 performed genomic analyses on 23 individuals from this site, and found that just about half of the remains were from individuals with South Asian ancestry, dated to ~800 CE. The authors concluded that they may have died while performing the Nanda Devi Raj Jat pilgrimage, suggesting that this religious practice may have existed in some form at this time in the past.…”

Section: Individual Journeys and Mobilitymentioning

confidence: 99%

Beyond broad strokes: sociocultural insights from the study of ancient genomes

et al. 2020

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The amount of sequence data obtained from ancient samples has dramatically expanded in the last decade, and so have the types of questions that can now be addressed using ancient DNA. In the field of human history, while ancient DNA has provided answers to long-standing debates about major movements of people, it has also recently begun to inform on other important facets of the human experience. The field is now moving from not only focusing on large-scale supra-regional studies to also taking a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this review, we summarize recent studies showcasing these types of insights, focusing on the methods used to infer sociocultural aspects of human behaviour. This work often involves working across disciplines that have, until recently, evolved in separation. We argue that multidisciplinary dialogue is crucial for a more integrated and richer reconstruction of human history, as it can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not have been possible to obtain otherwise.

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Section: Individual Journeys and Mobilitymentioning

confidence: 99%

Beyond broad strokes: sociocultural insights from the study of ancient genomes

et al. 2020

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“…This new type of qpAdm protocols, termed “rotating” protocol, has been adopted in archaeogenetics widely (see, e.g., Skoglund et al 2017, Harney et al 2019, Narasimhan et al 2019, Olalde et al 2019, Calhoff et al 2021, Fernandes et al 2021, Librado et al 2021, Allentoft et al 2022, Bergström et al 2022, Lazaridis et al 2022, Oliveira et al 2022, Taylor et al 2023). The most extreme version of the “rotating” protocol simply divides a set of reference populations into all possible combinations of “right” and “proxy source” subsets of certain sizes and rotates these combinations through successive qpAdm analyses.…”

Section: Introductionmentioning

confidence: 99%

Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

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Işıldak

Williams

et al. 2023

Preprint

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Although a broad range of methods exists for reconstructing population history from genome-wide single nucleotide polymorphism data, just a few methods gained popularity in archaeogenetics: principal component analysis (PCA); ADMIXTURE, an algorithm that models individuals as mixtures of multiple ancestral sources represented by actual or inferred populations; formal tests for admixture such as f3-statistics and D-statistics; and qpAdm, a tool for fitting two-component and more complex admixture models to groups or individuals. Despite their popularity in archaeogenetics, which is explained by modest computational requirements and ability to analyse data of various types and qualities, protocols relying on qpAdm that screen numerous alternative models of varying complexity and find "fitting" models (often considering both estimated admixture proportions and p-values as a composite criterion of model fit) remain untested on complex simulated population histories in the form of admixture graphs of random topology. We analysed genotype data extracted from such simulations and tested various types of high-throughput qpAdm protocols ("rotating" and "non-rotating", with or without temporal stratification of target groups and proxy ancestry sources, with or without a "model competition" step). We caution that these qpAdm protocols may be inappropriate for exploratory analyses in poorly studied regions/periods since their false discovery rates varied between 12% and 68% depending on the details of the protocol and on the amount and quality of simulated data (i.e., >12% of fitting two-way admixture models imply gene flows that were not simulated), although our study has a number of limitations. We demonstrate that for reducing false discovery rates of qpAdm protocols to nearly 0% it is advisable to use large SNP sets with low missing data rates, the rotating qpAdm protocol with a strictly enforced rule that target groups do not pre-date their proxy sources, and an unsupervised ADMIXTURE analysis as a way to verify feasible qpAdm models.

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“…However, analyzing ancient DNA (aDNA) poses additional difficulties due to the widely different but generally low genome coverage and postmortem damage (PMD) observed in these samples. The aDNA databases usually contain sequence data between 0.05 and 3× average genome coverage [ 10 – 12 ], since the sequencing of ancient samples with low endogenous DNA content is still challenging and costly. Differences in coverage and only partial overlap of genetic markers between samples can lead to significant bias when comparing the frequencies and genotype likelihoods of genetic variants, leading to uncertainties of the inferred genotype probabilities.…”

Section: Introductionmentioning

confidence: 99%

correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes

et al. 2023

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Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×–11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.

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Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India

Cited by 21 publications

References 74 publications

Beyond broad strokes: sociocultural insights from the study of ancient genomes

Beyond broad strokes: sociocultural insights from the study of ancient genomes

Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes

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