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 palaeogenomes. 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 (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K 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 5 K 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.

Human inbreeding has decreased in time through the Holocene.

The history of human inbreeding is controversial.1 In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels, relative to those of hunter-gatherer communities, is unclear.2-5 Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years.5-34 We show that the frequency of inbreeding, as measured by ROHs, 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 small population size instead of consanguinity. Cases of high consanguinity were rare and only observed among members of farming societies in our sample. Despite the lack of evidence for common consanguinity in our ancient sample, consanguineous traditions are today prevalent in various modern-day Eurasian societies,1,35-37 suggesting that such practices may have become widespread within the last few millennia.

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Asikli Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Asikli Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcin, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3-5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.

N1-P2: Neural markers of temporal expectation and response discrimination in interval timing.

Humans use temporal regularities in their daily life to act in accordance with future events in the most efficient way. To achieve this, humans build temporal expectations and determine a template action that is in line with those expectations. In this temporal trisection study, we aimed to study the neurophysiological counterparts of temporal expectation and response discrimination. We investigated amplitude variations of early event-related potentials (ERPs) while manipulating time intervals. We measured temporal expectation-related attenuation of neural activity and response discrimination processes in N1 and P2 ERP components. Results showed that the amplitude of the N1 component was attenuated for the predicted task-relevant temporal location of a response decision. The P2 amplitude, in contrast, was enhanced for a discriminated response in comparison to a template response. The present study supports a link between the different functional associations of the N1 and P2 components within the requirements of a timing task. N1-related amplitude modulation can determine a change in expectation level during timing. The amplitude regulation of the P2 component, in contrast, explains temporal discrimination in both expected and unexpected temporal locations. In addition to expectation­related modulation, our results suggest an additional regulation of the N1 amplitude that is linked to attention. The effect was observed in instances that included a prediction error of a task-relevant temporal location for a response decision. In conclusion, our study contributes to the growing neurocognitive literature on interval timing by capturing different aspects of a timing task; namely, N1-related expectation and P2-related response discrimination processes.

Brain Oscillatory Correlates of Visual Short-Term Memory Errors.

Brain dynamics of memory formation were explored during encoding and retention intervals of a visual working memory task. EEG data were acquired while subjects were exposed to grayscale images of widely known object categories (e.g., "luggage," "chair," and "car"). Following a short delay, two probes were shown to test memory accuracy. Oscillatory portraits of successful and erroneous memories were contrasted. Where significant differences were identified, oscillatory traits of false memories (i.e., when a novel probe item of the same category is recognized as familiar) were compared with those of successful and erroneous memories. Spectral analysis revealed theta (6-8 Hz) power over occipital channels for encoding of successful and false memories that was smaller when compared to other types of memory errors. The reduced theta power indicates successful encoding and reflects the efficient activation of the underlying neural assemblies. Prominent alpha-beta (10-26 Hz) activity belonging to the right parieto-occipital channels was identified during the retention interval. It was found to be larger for false memories and errors than that of correctly answered trials. High levels of alpha-beta oscillatory activity for errors correspond to poor maintenance leading to inefficient allocation of WM resources. In case of false memories, this would imply necessary cognitive effort to manage the extra semantic and perceptual load induced by the encoded stimuli.

Modulation of alpha oscillations is required for the suppression of semantic interference.

Recent findings on alpha band oscillations suggest their important role in memory consolidation and suppression of external distractors such as environmental noise. However, less attention was given to the phenomenon of internal distracting information being solely inherent to the stimuli content. Human memory may be prone to internal distractions caused by semantic relatedness between the meaning of words (e.g., atom, neutron, nucleus, etc.) to be encoded, i.e., semantic interference. Our study investigates the brain oscillatory dynamics behind the semantic interference phenomenon, whose possible outcome is known as false memories. In this direction, Deese-Roediger-McDermott word lists were appropriated for a modified Sternberg paradigm in auditory modality. Participants received semantically related and unrelated word lists via headphones while EEG data were acquired. Semantic interference triggered the false memory rates to be higher than those of other types of memory errors. Analysis demonstrated that the upper part of alpha band (∼10-12Hz) power decreases on parieto-occipital channels in the retention interval, prior to the probe item for semantically related condition. Our study elucidates the oscillatory mechanisms behind semantic interference by relying on alpha functional inhibition theory.