Biology subjects

Vural, K. B.

Publications and source records attributed to Vural, K. B..

15 recordsLinked to original sources

bioRxiv2025

The mini yet mighty stapes: a comparison of ancient DNA yields among ossicles and the petrous bone

The petrous bone is considered the most efficient source of endogenous DNA across skeletal tissues in ancient DNA research as well as in forensic work. Recently, ancient DNA (aDNA) in auditory ossicle bones was shown to be comparably well-preserved as in the petrous, although no attempt was made to distinguish among the three ossicle bones. In this study, we used a total of 114 human ossicle- and petrous-derived sequencing libraries from similar contexts (c.10,000 BP - 7,000 BP Anatolia), including 34 matched libraries prepared from the same individuals ossicle and petrous bones. Our results suggest that endogenous human aDNA preservation in the stapes is on average two times higher than in the petrous bone; it also tends to be higher than in the malleus and incus. Similarly, aDNA fragment lengths were higher in the stapes than in the petrous, whereas postmortem damage, clonality and contamination rates were comparable. Despite being the smallest bone in the human skeleton, the stapes may be the most optimal aDNA source yet identified.

genetics↗

bioRxiv2024

An age-specific burial practice reflected in ancient DNA preservation in Neolithic Catalhöyük

Selective funerary practices can inform about social relationships in prehistoric societies but are often difficult to discern. Here we present evidence for an age-specific practice at the Neolithic site of Catalhoyuk in Anatolia, dating to the 7th millennium BCE. Among ancient DNA libraries produced from 362 petrous bone samples, those of subadults contained three times higher average human DNA than those of adults. This difference in organic preservation was also confirmed by FTIR analysis. Studying similar datasets from seven prehistoric and historical sites, we found a similar age-related difference in only one cemetery. We propose that the organic preservation difference with age was caused by the special treatment of chosen corpses before interment, such as defleshing or drying, which was more frequently applied to Catalhoyuk adults and promoted organic decay.

evolutionary biology↗

bioRxiv2024

Ancient DNA analyses of two Early Chalcolithic Individuals from the West Mound

In this chapter, we investigate the genetics of two Early Chalcolithic Catalhoyuk individuals, U.18333 and U.16835, the only two burials yet recovered from the West Mound. These were two neonates buried within the same building. Using shotgun-sequenced partial genomes (0.06x and 0.02x coverage) we identify both as females. Despite being recovered from the same building, we find no close genetic kinship between them, in line with previously published kinship results from Catalhoyuk. We also find that the two West Mound neonates shared the same gene pool with Neolithic Catalhoyuk and other Central and West Anatolian Neolithic populations, and they did not carry the Caucasus-related "eastern" gene flow signature observed in later-coming Chalcolithic Anatolian genomes. This indicates no large-scale admixture between East and West Mound Catalhoyuk, and possibly that the post-Neolithic "eastern" gene flow event into Anatolia may have initiated only by the mid-6th millennium BCE.

genetics↗

bioRxiv2024

DeepKin: Predicting relatedness from low-coverage genomes and paleogenomes with convolutional neural networks

DeepKin is a novel tool designed to predict relatedness from genomic data using convolutional neural networks (CNNs). Traditional methods for estimating relatedness often struggle when genomic data is limited, as with paleogenomes and degraded forensic samples. DeepKin addresses this challenge by leveraging two CNN models trained on simulated genomic data to classify relatedness up to the third-degree and to identify parent-offspring and sibling pairs. Our benchmarking shows DeepKin performs comparably or better than the widely used tool READv2. We validated DeepKin on empirical paleogenomes from two paleological sites, demonstrating its robustness and adaptability across different genetic backgrounds, with accuracy >90% above 10K shared SNPs. By capturing information across genomic segments, DeepKin offers a new methodological path for relatedness estimation in settings with highly degraded samples, with applications in ancient DNA, as well as forensic and conservation genetics.

bioinformatics↗

bioRxiv2024

Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

Western Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. Using 30 new palaeogenomes from Anatolia c.8000-6000 BCE we describe the early Holocene genetic landscape of Western Anatolia, which reveals population continuity since the late Upper Pleistocene. Our findings indicate that the Neolithisation of Western Anatolia in the 7th millennium BCE was a multifaceted process, characterised by the assimilation of Neolithic practices by indigenous groups and the influx of populations from the east, their admixed descendants eventually laying the foundations of Neolithic Southeast Europe. Intriguingly, the observed diversity in material culture among Aegean Early Neolithic communities correlates with their geographical distances but not their genetic differences, signifying a decoupling between cultural developments and genetic admixture processes.

genomics↗

bioRxiv2024

Female lineages and changing kinship patterns in Neolithic Catalhöyük

Arguments have long suggested that the advent of early farming in the Near East and Anatolia was linked to a Mother Goddess cult. However, evidence for a dominant female role in these societies has been scarce. We studied social organisation, mobility patterns and gendered practices in Neolithic Southwest Asia using 131 paleogenomes from Catalhoyuk East Mound (7100-5950 BCE), a major settlement in Central Anatolia with an uninterrupted occupation and an apparent egalitarian structure. In contrast to widespread genetic evidence for patrilocality in Neolithic Europe, the Catalhoyuk individuals revealed no indication of patrilocal mobility. Analysing genetic kin ties among individuals buried in the same house (co-burials) across 35 Catalhoyuk buildings, we identified close ties concentrated within buildings and among neighbours in Catalhoyuks Early period, akin to those in the preceding Pre-Pottery Neolithic in Southwest Asia. This pattern weakened over time: by the late 7th millennium BCE, subadults buried in the same building were rarely closely genetically related, despite sharing similar diets. Still, throughout the sites occupation, genetic connections within Catalhoyuk buildings were much more frequently connected via the maternal than the paternal line. We also identified differential funerary treatment of female subadults compared to those of males, with a higher frequency of grave goods associated with females. Our results reveal how kinship practices changed while key female roles persisted over one thousand years in a large Neolithic community in western Eurasia.

genomics↗

bioRxiv2024

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

The possibility to obtain genome-wide ancient DNA data from multiple individuals has facilitated an unprecedented perspective into prehistoric societies. Studying biological relatedness in these groups requires tailored approaches for analyzing ancient DNA due to its low coverage, post-mortem damage, and potential ascertainment bias. Here we present READv2 (Relatedness Estimation from Ancient DNA version 2), an improved Python 3 re-implementation of the most widely used tool for this purpose. While providing increased portability and making the software future-proof, we are also able to show that READv2 (a) is orders of magnitude faster than its predecessor; (b) has increased power to detect pairs of relatives using optimized default parameters; and, when the number of overlapping SNPs is sufficient, (c) can differentiate between full-siblings and parent-offspring, and (d) can classify pairs of third-degree relatedness. We further use READv2 to analyze a large empirical dataset that has previously needed two separate tools to reconstruct complex pedigrees. We show that READv2 yields results and precision similar to the combined approach but is faster and simpler to run. READv2 will become a valuable part of the archaeogenomic toolkit in providing an efficient and user-friendly classification of biological relatedness from pseudohaploid ancient DNA data.

bioinformatics↗

bioRxiv2023

Population genomic history of the endangered Anatolian and Cyprian mouflons in relation to worldwide wild, feral and domestic sheep lineages

Once widespread in their homelands, Anatolian mouflon (Ovis gmelini anatolica) and Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the IUCN. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep groups. Here, we study whole genome sequences of n=5 Anatolian mouflons and n=10 Cyprian mouflons in terms of population history and diversity, relative to eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (Ovis gmelini). Despite similar recent population dynamics, Anatolian and Cyprian mouflons exhibit disparate diversity levels, which can potentially be attributed to founder effects, island isolation, introgression from domestic lineages, or different bottleneck dynamics. The lower relative mutation load found in Cyprian compared to Anatolian mouflons suggests the purging of recessive deleterious variants in the former. This agrees with estimates of a long-term small effective population size in the Cyprian mouflon. Both subspecies harbor considerable numbers of runs of homozygosity (ROH) blocks <2 Mb, which reflects the effect of small population size. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages, and a limited consistency between viability metrics and conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may contribute to the observed disparities.

evolutionary biology↗

bioRxiv2023

Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome data

Ancient DNA analysis is subject to various technical challenges, including bias towards the reference allele ("reference bias"), postmortem damage (PMD) that confounds real variants, and limited coverage. Here, we conduct a systematic comparison of alternative approaches against reference bias and against PMD. To reduce reference bias, we either (a) mask variable sites before alignment or (b) align the data to a graph genome representing all variable sites. Compared to alignment to the linear reference genome, both masking and graph alignment effectively remove allelic bias when using simulated or real ancient human genome data, but only if sequencing data is available in FASTQ or unfiltered BAM format. Reference bias remains indelible in quality-filtered BAM files and in 1240K-capture data. We next study three approaches to overcome postmortem damage: (a) trimming, (b) rescaling base qualities, and (c) a new algorithm we present here, bamRefine, which masks only PMD-vulnerable polymorphic sites. We find that bamRefine is optimal in increasing the number of genotyped loci up to 20% compared to trimming and in improving accuracy compared to rescaling. We propose graph alignment coupled with bamRefine to minimise data loss and bias. We also urge the paleogenomics community to publish FASTQ files.

bioinformatics↗

bioRxiv2023

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations

There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage paleogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD-estimation methods and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1K to 50K) of shared SNPs (with minor allele frequency [≥]0.01) are available. The performance of all four tools was comparable using [≥]20K SNPs. We found that first-degree related pairs can be accurately classified even with 1K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 >90%) with 5K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69% and 79%, respectively). Meanwhile, noise in population allele frequencies and inbreeding (first cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low coverage genomes.

genetics↗

bioRxiv2023

The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus)

We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1st millennium BCE, sequenced to coverages of 0.6-6.4X. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass. The Anatolian wild ass whole genome profiles fall outside the genomic diversity of other extant and past Asiatic wild ass (E.hemionus) lineages. These observations strongly suggest that the three Anatolian wild asses represent E.hydruntinus, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Comparative genomic analyses suggest that E.hydruntinus was a sister clade to all ancient and present-day E.hemionus lineages, representing an early split. We also find indication of gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity reveal that the Anatolian wild ass population had severely lost genetic diversity by the mid-1st millennium BCE, a likely omen of its eventual demise.

genomics↗

bioRxiv2022

MTaxi : A comparative tool for taxon identification of ultra low coverage ancient genomes

A major challenge in zooarchaeology is to morphologically distinguish closely related species remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.5x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity with mtDNA coverages 0.1x - 12x also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are compelling to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.

bioinformatics↗

bioRxiv2022

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Cayonu in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Cayonu was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Cayonus cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamias cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.

genetics↗

bioRxiv2020

Human inbreeding has decreased in time through the Holocene

The history of human inbreeding is controversial. The development of sedentary agricultural societies may have had opposite influences on inbreeding levels. On the one hand, agriculture and food surplus may have diminished inbreeding by increasing population sizes and lowering endogamy, i.e. inbreeding due to population isolation. On the other hand, increased sedentism, as well as the advent of private property may have promoted inbreeding through the emergence of consanguineous marriage customs or via ethnic and caste endogamy. The net impact is unknown, and to date, no systematic study on the temporal frequency of inbreeding in human societies has been conducted. Here we present a new approach for reliable estimation of runs of homozygosity (ROH) in genomes with [≥]3x mean coverage across >1 million SNPs, and apply this to 440 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to endogamy, although singular cases of high consanguinity can also be found in the archaeogenomic record. HighlightsA study of 440 ancient genomes shows inbreeding decreased over time. The decrease appears linked with population size increase due to farming. Extreme consanguineous matings did occur among farmers, but rarely.

genomics↗

bioRxiv2020

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Sheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central and west Anatolian sheep dating to the Late Glacial and early Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, mitochondrial haplogroup diversity increases, compatible with admixture from other domestication centres and/or from wild populations. Analysing archaeogenomic data, we further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds, and especially those from central and north Europe. Our results indicate that Asian contribution to south European breeds in the post-Neolithic era, possibly during the Bronze Age, may explain this pattern.

evolutionary biology↗