Benchmarking kinship estimation tools for ancient genomes using pedigree simulations

Date

2020-10-22

Author

Çetin, Mehmet
Aktürk, Şevval
Mapelli, Igor
Yaka, Reyhan
Çokoğlu, Seda
Zakaria, Douaa
Ceballos, Francisco
Ghalichi, Ayshin
Altınışık, N. Ezgi
Koptekin, Dilek
Vural, Kıvılcım Başak
Erdal, Yılmaz Selim
Atakuman, Çiğdem
Götherström, Anders
Özer, Füsun
Sürer, Elif
Somel, Mehmet

Metadata

Show full item record

Item Usage Stats

490
views

0
downloads

There is growing interest in identifying genetic kinship levels among ancient individuals buried in physical proximity, from graveyards to archaeological crime scenes. Ancient genome data produced using massively parallel sequencing allow such estimation, albeit with significant limitations owing to the extremely low coverage of ancient genomes, frequently ranging between 0.2x - 0.01x. Estimating the kinship coefficient reliably using such sparse data is a challenge. Both likelihood-based and non-parametric tools have been recently developed to address this question, but their efficiency has not yet been systematically and comparatively studied. Here we present work where we compared the accuracy of three most commonly employed tools, using ancient genome data produced from simulated pedigrees. We studied accuracy with respect to both kinship coefficient estimation, and also Cotterman coefficients. Our results show that genotype data that include >5,000 SNPs allow close kinship coefficients to be relatively reliably estimated, although accuracy falls dramatically beyond the 3rd degree. In addition, we confirm that pedigree relationship estimation (e.g. distinguishing between parent-child pairs vs. siblings) using Cotterman coefficients is a noteworthy problem, and will require alternative, and holistic approaches to address.

URI

https://hdl.handle.net/11511/80731

Collections

Unverified, Conference / Seminar

Suggestions

OpenMETU
Core

Evaluation of protective structures in archaeological sites for in situ conservation of achitectural remains and artifacts Ertosun, Atiye Işıl; Özgönül, Nimet; Restoration in Department of Architecture (2012) Artifacts are moved to museums after the excavations in order to provide an indoor protection, while the immovable findings remain exposed to environmental conditions and human activity. In order to conserve these architectural remains made of vulnerable material, mosaics and wall paintings in situ, covering structures are designed offering temporary or long-term sheltering, preserving and exhibiting facilities. The aim of the study is to evaluate these protective structures. In this study, national and int...
ASSESSING THE IMPACT OF HERITAGE-LED URBAN REGENERATION PROJECTS ON THE HISTORIC CITY CENTER OF ANTAKYA Nemati, Parnian; Aykaç Leıdholm, Pınar; Rifaioğlu, Mert Nezih; Conservation of Cultural Heritage in Department of Architecture (2022-12-13) The worldwide phenomenon of heritage-led regeneration has been considered a panacea for dilapidated historic urban tissues to regenerate them through their cultural heritage. However, the promotion of the heritage through development plans and projects affects the physical and social aspects of historic urban tissues substantially. Therefore, it is necessary to assess the precise impacts of heritage-led regeneration due to its extensive effects on historic cities and residents. Antakya, or ancient Antioch, ...
Sanctifying the House Child Burial in Prehistoric Anatolia Yıldırım, Burcu; Hackley, Laurel D.; Steadman, Sharon R. (University of Chicago Press, 2018-09-01) The intramural burial of small children is culturally widespread, seen from prehistory until modern times n many places around the world. The practice was especially common in the prehistoric eastern Mediterranean, with many examples found in in Egypt, the Levant, and Anatolia. Burial of individuals within the house suggests kinship connections with the dead, the connection of the physical home to the life of the family, and perhaps the belief that the presence of buried family members protected the living.
Characterisation of DNA from archaelogical wheat (Triticum L.) seeds from Anatolia Somel, Mehmet; Kence, Aykut; Akkaya, Mahinur S.; Department of Biotechnology (2003) Ancient DNA analysis of archaeological wheat remains may serve to clarify unknown or controversial points in the history of wheat. In the first part of this study, extraction and amplification of DNA from Anatolian charred ancient wheat seeds obtained from different locations and ages was attempted. None of the our extraction samples yielded any PCR amplification. The possible reasons for this result were investigated by constructing an artificial charring experiment. The results suggest that the chances of...
"Not All That Is White Is Lime'-White Substances from Archaeological Burial Contexts: Analyses and Interpretations Schotsmans, Eline M J; Toksoy Köksal, Fatma; Brettell, R. C.; Bessou, Maryelle; Corbineau, Remi; Lingle, Ashley M; Bouquin, D.; Blanchard, P.; Becker, K.; Castex, D.; Knusel, C. J.; Wilson, A. S.; Chapoulie, R. (2019-08-01) Archaeological burial contexts may include a variety of white substances, but few analyses have been published. This study reports on the physico-chemical characterization of such residues from seven archaeological sites. It is often assumed that white materials from burial contexts are lime. Our findings demonstrate that they can be gypsum, calcite (chalk), aragonite, brushite, degraded metal, natural (gum) resins or synthetic polymer-based products. These may be present as the result of diagenetic process...

Citation Formats

M. Çetin et al., “Benchmarking kinship estimation tools for ancient genomes using pedigree simulations,” 2020, Accessed: 00, 2021. [Online]. Available: https://hdl.handle.net/11511/80731.