Ancient DNA sheds light on the genetic origins of early Iron Age Philistines

Feldman, Michal; Master, Daniel M.; Bianco, Raffaela A.; Burri, Marta; Stockhammer, Philipp W.; Mittnik, Alissa; Aja, Adam J.; Jeong, Choongwon; Krause, Johannes

doi:10.1126/sciadv.aax0061

Cited by 72 publications

(74 citation statements)

References 61 publications

(115 reference statements)

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“…The role of Sea People may therefore be crucial in explaining a temporary presence of a Minoan-like ancestry in the Levant, bringing Anatolian-like components to levels as high as 85%. A pulse of populations with Anatolian-rich ancestry has just been recently detected in Iron Age Levant, appearing and disappearing from the archaeological record within a range of few centuries 13 . Our results offer a solution to this disappearance, given that their signal may have become erased as a consequence of major warfare after 1000 BCE 14 , bringing these genetic components towards Ethiopia and North Africa.…”

Section: Resultsmentioning

confidence: 99%

West Asian sources of the Eurasian component in Ethiopians: a reassessment

Molinaro

Montinaro

Kivisild

et al. 2019

Preprint

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Previous genome-scale studies of populations living today in Ethiopia have found evidence of 1 recent gene flow from an Eurasian source, dating to the last 3,000 years 1,2,3,4 . Haplotype 1 2 and genotype data based analyses of modern 2,4 and ancient data (aDNA) 3,5 have considered 3 Sardinia-like proxy 2 , broadly Levantine 1,4 or Neolithic Levantine 3 populations as a range of 4 possible sources for this gene flow. Given the ancient nature of this gene flow and the extent 5 of population movements and replacements that affected West Asia in the last 3000 years, 6 aDNA evidence would seem as the best proxy for determining the putative population source. 7 We demonstrate, however, that the deeply divergent, autochthonous African component which 8 accounts for ∼50% of most contemporary Ethiopian genomes, affects the overall allele frequency 9 spectrum to an extent that makes it hard to control for it and, at once, to discern between 10 subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). 11Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here 12 called "NAF" for Non African) and ancient and modern proxies area after having extracted NAF 13 from Ethiopians through ancestry deconvolution, and unveil a genomic signature compatible 14 with population movements that affected the Mediterranean area and the Levant after the fall 15 of the Minoan civilization. 16 Results and Discussion 17To determine the most likely source of the Eurasian gene flow into the ancestral gene pool of 18 present-day Ethiopians we have used a combination of ancestry deconvolution (AD) and allele 19 sharing methods 6 . AD refers to analyses that determine the likeliest ancestry composition of 20 genomes of individuals with mixed ancestry at fine haplotype resolution. These methods have 21 1 allowed us to i) exploit high quality modern data and ii) harness the power of allele sharing 22 tools on genetic fractions with no or reduced African contributions. Such a strategy, while 23 potentially beneficial, introduce a novel source of bias which we aimed to explore here. Par-24 ticularly, after AD of 120 Ethiopian genomes 7 , we assigned each genomic SNP into one of the 25 following four categories based on the method likelihoods (see Methods for further details): 1) 26 confidently non African (NAF); 2) low confidence non African (X); 3) low confidence African 27 (Y) and 4) confidently African (AF, consistently filtered out from our analyses). While basing 28 our inference on the NAF component alone, we here demonstrate that the component X does 29 account for a minority of the genome and, when analysed together with NAF does not quali-30 tatively change the results. Furthermore, when joining together the NAF and AF confidently 31 assigned components (to create "Joint" components) we recapitulate the signals of the global 32 population (prior to ancestry deconvolution), showing that the X and Y components are not 33 holding a considerable or peculiar genetic signat...

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Section: Resultsmentioning

confidence: 99%

West Asian sources of the Eurasian component in Ethiopians: a reassessment

Molinaro

Montinaro

Kivisild

et al. 2019

Preprint

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“…Based on previous successes in DNA recovery, the petrous pyramid is currently the most soughtafter skeletal element for aDNA analyses [21][22][23][24][25]40,41 . Our investigation of multiple skeletal elements further confirms the value of the petrous pyramid in the recovery of ancient human DNA (Figure 2A-C).…”

Section: Discussionmentioning

confidence: 99%

“…This observation is based on a collection of comparative PCR 15,[17][18][19][20] and whole genome aDNA surveys [16][17][18] that were, however, limited in the number of individuals and/or skeletal elements tested. Despite the absence of a systematic comparative analysis of preservation across the skeleton, aDNA obtained from the petrous portions of human remains has been utilized to great success in the contexts of both ancient human population genetics [21][22][23][24][25] and forensic investigations 12,24,25 .…”

Section: Introductionmentioning

confidence: 99%

“…libraries are of sufficient complexity and show low signals of contamination with present-day human DNA. The aDNA libraries produced in this study were not sequenced to exhaustion, and as a consequence duplication rates were too low to be informative in terms of estimating library complexity in both the pre-enrichment libraries (average duplication factor 1 21). and the post-capture libraries (average duplication factor 1.22) (see Supplementary File 1:Duplication factor).…”

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A systematic investigation of human DNA preservation in medieval skeletons

Parker

Rohrlach

Friederich

et al. 2020

Preprint

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Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material.Currently the dense inner portion of the petrous pyramid, the location of the skull that houses the inner ear, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. Destructive sampling of the petrous pyramid, assuming its recovery, is often not recommended for highly valued specimens. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies. 2 26 27 28 29 30 31 32 33 34 35 36 37 38Recent advances in minimally invasive sampling techniques 26 have led to a better balance between preservation of the anthropological record and the need for the production of reliable genetic data 27,28 ; however, the threat of damage to internal microstructures that form an important basis of morphological assessments 29-31 can still introduce hesitancy on the part of curators and physical anthropologists in making the petrous pyramid available for aDNA applications. These factors, in conjunction with the chance of incomplete recovery of crania at excavation 32 or restricted sampling of highly valued specimens, make the identification of alternative sampling locations based on quantitative evaluations of DNA preservation across the skeleton of clear benefit. Teeth have been widely used for the study of aDNA 33,34 , though the 30-fold covered genome of an archaic hominin from Denisova Cave from a distal phalanx demonstrates molecular preservation in elements that are not typically considered for paleogenetics work 4 . Despite these successes, a systematic and extensive study of differential DNA preservation across multiple human skeletal elements, such as those done in the context of modern forensics 35,36 , has yet to be attempted on archaeological remains. Our limited understanding of DNA preservation across the human skeleton is a significant hurdle for the efficient, practical, and ethical study of aDNA, which has particular relevance to the field of ancient population genetics where large sample sizes are needed for robust analytical resolution.DNA preservation can be influenced by many factors including burial practises and treatment of the deceased, geology, as well as environmental and climatic conditions 37 , where the chronological age of a sample is thought to play only a secondary role 38,39 . To serve as a baseline for future investigations seeking to incorporate and extrapolate the effects of these sources of v...

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“…Last month, for example, the publication of an aDNA study of Bronze and Iron Age populations from the Levantine port city of Ashkelon (Feldman et al . 2019) attracted significant media attention. The results were swiftly critiqued on social media for the framing of the research questions, choice of samples and contextualisation of the results; they were also explicitly politicised through the lens of regional politics (not helped by the emphasis on ‘Philistines’ in the article title, which poorly reflects the contents).…”

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confidence: 99%

From the wisdom of old age to a wider debate

Witcher

2019

Antiquity

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Ancient DNA sheds light on the genetic origins of early Iron Age Philistines

Cited by 72 publications

References 61 publications

West Asian sources of the Eurasian component in Ethiopians: a reassessment

West Asian sources of the Eurasian component in Ethiopians: a reassessment

A systematic investigation of human DNA preservation in medieval skeletons

From the wisdom of old age to a wider debate

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