The diverse genetic origins of a Classical period Greek army

Reitsema, Laurie J; Mittnik, Alissa; Kyle, Britney; Catalano, Giulio; Fabbri, Pier Francesco; Kazmi, Adam C. S.; Reinberger, Katherine L; Sìneo, Luca; Vassallo, Stefano; Bernardos, Rebecca; Broomandkhoshbacht, Nasreen; Callan, Kim; Candilio, Francesca; Cheronet, Olivia; Curtis, Elizabeth; Fernandes, Daniel; Lari, Martina; Lawson, Ann Marie; Mah, Matthew; Mallick, Swapan; Mandl, Kirsten; Micco, Adam; Modi, Alessandra; Oppenheimer, Jonas; Özdoğan, Kadir T.; Rohland, Nadin; Stewardson, Kristin; Vai, Stefania; Vergata, Chiara; Workman, J Noah; Zalzala, Fatma; Zaro, Valentina; Achilli, Alessandro; Anagnostopoulos, Achilles; Capelli, Cristian; Constantinou, Varnavas; Lancioni, Hovirag; Olivieri, Anna; Παπαδοπούλου, Αναστασία; Psatha, Nikoletta; Semino, Ornella; Stamatoyannopoulos, J; Valliannou, Ioanna; Yannaki, Evangelia; Lazaridis, Iosif; Patterson, Nick; Ringbauer, Harald; Caramelli, David; Pinhasi, Ron; Reich, David

doi:10.1073/pnas.2205272119

Cited by 19 publications

(31 citation statements)

References 79 publications

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“…The population of Southern Italy has strong genetic connections to those of the Eastern Mediterranean, due to Greek colonisation in archaic times [ 149 ], as well as to later demographic events during Imperial Roman and Medieval times, which transformed the entire peninsula [ 150 , 151 ]. The Greek-speakers of Apulia and Calabria speak two Greek dialects that date back to the early Middle Ages [ 152 , 153 ], but retain numerous influences from a native Doric substrate [ 153 – 155 ].…”

Section: Results 1: the Dominant Zoonyms Of Bufo Bufo ...mentioning

confidence: 99%

Toad zoonyms mirror the linguistic and demographic history of Greece

Davranoglou

Embirikos

2023

PLoS ONE

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The common toad (Bufo bufo) has been the subject of many folk tales and superstitions in Western Europe, and as a result, it is characterised by numerous common names (zoonyms). However, the zoonyms of the toad and its associated traditions have remained unexplored in the Balkans, one of Europe’s linguistic hotspots. In the present study, it was attempted to fill this knowledge gap by focusing on Greece, where more than 7.700 individuals were interviewed both in the field and through online platforms, in order to document toad zoonyms from all varieties and dialects of Greek, as well as local non-Greek languages such as Arvanitika, South Slavic dialects, and Vlach. It was found that the academically unattested zoonyms of the toad provide an unmatched and previously unexplored linguistic and ethnographic tool, as they reflect the linguistic, demographic, and historical processes that shaped modern Greece. This is particularly pertinent in the 21st century, when a majority of the country’s dialects and languages are in danger of imminent extinction–and some have already gone silent. Overall, the present study shows the significance of recording zoonyms of indigenous and threatened languages as excellent linguistic and ethnographic tools that safeguard our planet’s ethnolinguistic diversity and enhance our understanding on how pre-industrial communities interacted with their local fauna. Furthermore, in contrast to all other European countries, which only possess one or only a few zoonyms for the toad, the Greek world boasts an unmatched 37 zoonyms, which attest to its role as a linguistic hotspot.

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Section: Results 1: the Dominant Zoonyms Of Bufo Bufo ...mentioning

confidence: 99%

Toad zoonyms mirror the linguistic and demographic history of Greece

Davranoglou

Embirikos

2023

PLoS ONE

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“…A base peak chromatogram (300−1600 m/z ) with two marked peptides of amelogenin: AMELY‐[58–64] and AMELX‐[44–52]. The reconstructed ion chromatograms (to 4 ppm) for each are shown in red and blue; full‐scan MS and corresponding MS/MS are shown below.…”

Section: Proteomic Estimation Of Sexmentioning

confidence: 99%

“…The current rapid development of genomics will certainly enable even more sophisticated methods of genetic sex estimation. Current research is yielding very encouraging results in the field of archeology that were previously unavailable (i.e., [46–48]).…”

Section: Genetic Estimation Of Sexmentioning

confidence: 99%

Peptide analysis of tooth enamel – A sex estimation tool for archaeological, anthropological, or forensic research

Mikšı́k

Morvan

Brůžek

2023

J of Separation Science

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Proteomics has become an attractive method to study human and animal material, biological profile, and origin as an alternative to DNA analysis. It is limited by DNA amplification in ancient samples and its contamination, high cost, and limited preservation of nuclear DNA. Currently, three approaches are available to estimate sex–osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. Proteomics provides a new, seemingly simple, and relatively non‐expensive way of sex estimation without the risk of contamination. Proteins can be preserved in hard teeth tissue (enamel) for tens of thousands of years. It uses two sexually distinct forms of the protein amelogenin in tooth enamel detectable by liquid chromatography‐mass spectrometry; the protein amelogenin Y isoform is present in enamel dental tissue only in males, while amelogenin isoform X can be found in both sexes. From the point of view of archaeological, anthropological, and forensic research and applications, the reduced destruction of the methods used is essential, as well as the minimum requirements for sample size.

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“…Nonetheless, most current studies (e.g. Allentoft et al, 2015; Scheib et al, 2018; Margaryan et al, 2020; Furtwängler et al, 2020; Lipson et al, 2022; Liu et al, 2022b; Reitsema et al, 2022) use the same thresholds for sexing without considering differences in sequencing methods, sequencing depth or sample treatment.…”

Section: Introductionmentioning

confidence: 99%

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

Caduff,

Eckel,

Leuenberger

et al. 2023

Preprint

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The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it estimates the sex karyotype posterior probabilities also for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient humans as well as several non-model organisms.

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The diverse genetic origins of a Classical period Greek army

Cited by 19 publications

References 79 publications

Toad zoonyms mirror the linguistic and demographic history of Greece

Toad zoonyms mirror the linguistic and demographic history of Greece

Peptide analysis of tooth enamel – A sex estimation tool for archaeological, anthropological, or forensic research

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

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