Biology subjects

Konig, P.

Publications and source records attributed to Konig, P..

5 recordsLinked to original sources

bioRxiv2025

Efficient Phylogenetic Inference Using SNP-Based Approaches: A Comparison with Full Sequence Data

Mutations in specific genomic regions or genes serve as reliable indicators of phylogenetic relationships, with single nucleotide polymorphisms (SNPs) playing a crucial role in population phylogenetic studies. Traditional distance-based phylogenetic algorithms have a time complexity proportional to l n2, where n is the number of sequences and l is their length [1], [2]. This high computational cost becomes a bottleneck in phylogeny reconstruction, particularly when l > n. To overcome this limitation, we propose an SNP-based approach to phylogenetic tree inference, focusing exclusively on variant (mutated) positions rather than entire sequences. This method significantly reduces computational time while maintaining accuracy. We compare phylogenies inferred from SNP data and full sequence data (including both SNPs and invariant sites) across multiple metrics. Our results show that heuristic phylogenetic trees constructed from SNPs achieve parsimony scores nearly identical to those derived from full sequence data, as parsimony primarily depends on variant positions. Additionally, under the Jukes-Cantor 1969 (JC69) model, log-likelihood scores for SNP-based and full-sequence-based trees exhibit a strong correlation when evaluated using the same tree topology, branch lengths, and maximum likelihood parameters. These findings demonstrate that SNP-based methods can streamline phylogenetic analysis while preserving accuracy.

bioinformatics↗

bioRxiv2024

The impact of human agents on spatial navigation and knowledge acquisition in a Virtual Environment

Concepts of spatial navigation rest on the idea of landmarks, which are immobile features or objects in the environment. However, behaviorally relevant objects or fellow humans are often mobile. This raises the question of how the presence of human agents influences spatial exploration and knowledge acquisition. Here, we investigate exploration and performance in subsequent spatial tasks within a virtual environment containing numerous human avatars. In the exploration phase, agents had a locally limited effect on navigation. They prompted participants to revisit locations with agents during their initial exploration without significantly altering overall exploration patterns or the extent of the area covered. However, agents and buildings competed for visual attention. When spatial recall was tested, pointing accuracy toward buildings improved when participants directed their attention to the buildings and nearby agents. In contrast, pointing accuracy for agents showed weaker performance and did not benefit from visual attention directed toward the adjacent building. Active agents and incongruent agent-environment pairings further enhanced pointing accuracy, revealing that violations of expectations by agents can significantly shape navigational knowledge acquisition. Overall, agents influenced spatial exploration by directing attention locally, with the interaction between agent salience and environmental features playing a key role in shaping navigational knowledge acquisition.

neuroscience↗

bioRxiv2023

Improved spatial knowledge acquisition through sensory augmentation

Sensory augmentation offers a novel opportunity to broaden our knowledge of human perception through the use of external sensors that record information that humans cannot perceive naturally. This information is then translated in a meaningful way to be presented through an inherent sensory modality. To assess whether such augmented senses affect the acquisition of spatial knowledge during navigation, we trained a group of 26 participants for six weeks with an augmented sense for cardinal directions, called the feelSpace belt. In order to assess perceptual and behavioral changes, we compared the use of spatial strategies and the spatial navigation performance of the belt group to the performance of a control group that did not receive the augmented sense or the training. To this end, all participants explored the virtual reality environment Westbrook for 150 minutes in total. Then, the participants spatial knowledge of the virtual reality city was assessed subjectively with the FRS questionnaire and behaviorally in four immersive virtual reality tasks within Westbrook. The belt group reported a significant increase in the use of spatial strategies after training, while the groups ratings were comparable at baseline. The finding is consistent with previous studies showing cognitive and subjective changes to space perception as a consequence of wearing the feelSpace belt for an extended time period. Behaviorally, we found that the belt group acquired significantly more accurate knowledge of cardinal directions and of survey knowledge, measured in pointing accuracy, distance and rotation estimates. Finally, we found that the augmented sense also positively affects route knowledge but to a lesser degree. These results suggest that six weeks of training with the feelSpace belt lead to an improved acquisition of survey and route knowledge as reflected by an increased accuracy in survey and route knowledge tasks in a virtual city.

neuroscience↗

bioRxiv2017

Are allocentric spatial reference frames compatible with theories of Enactivism?

Theories of Enactivism propose an action-oriented approach to understand human cognition. So far, however, empirical evidence supporting these theories has been sparse. Here, we investigate whether spatial navigation based on allocentric reference frames that are independent of the observers physical body can be understood within an action-oriented approach. Therefore, we performed three experiments testing the knowledge of the absolute orientation of houses and streets towards north, the relative orientation of two houses and two streets, respectively, and the location of houses towards each other in a pointing task. Our results demonstrate that under time pressure, the relative orientation of two houses can be retrieved more accurately than the absolute orientation of single houses. With infinite time for cognitive reasoning, the performance of the task using house stimuli increased greatly for the absolute orientation and surpassed the slightly improved performance in the relative orientation task. In contrast, with streets as stimuli participants performed under time pressure better in the absolute orientation task. Overall, pointing from one house to another house yielded the best performance. This suggests, firstly, that orientation and location information about houses are primarily coded in house-to-house relations, whereas cardinal information is deduced via cognitive reasoning. Secondly, orientation information for streets is preferentially coded in absolute orientations. Thus, our results suggest that spatial information about house and street orientation is coded differently and that house orientation and location is primarily learned in an action-oriented way, which is in line with an enactive framework for human cognition.

neuroscience↗

bioRxiv2017

Pupil Size Asymmetries Are Modulated By An Interaction Between Attentional Load And Task Experience

In a recently published study [1], we investigated how human pupil sizes are modulated by task experience as well as attentional load in a visuospatial task. In particular, participants performed a multiple object tracking (MOT) task while pupil sizes were recorded using binocular eyetracking measurements. To vary the attentional load, participants performed the MOT task either tracking zero or up to five targets. To manipulate the task experience, participants performed the MOT task on three consecutive days. We found that pupil sizes systematically increased with attentional load and decreased with additional task experience. For all these analyses, we averaged across the pupil sizes for the left and right eye. However, findings of a recent study [2] have suggested that also asymmetries in pupil sizes could be related to attentional processing. Given these findings, we further analyzed our data to investigate to what extent pupil size asymmetries are modulated by attentional load and task experience. We found a significant interaction effect between these two factors. That is, on the first day of the measurements, pupil size asymmetries were not modulated by attentional load while this was the case for the second and third day of the measurements. In particular, for the second and third day, pupil size asymmetries systematically increased with attentional load, indicating that attentional processing also modulates pupil size asymmetries. Given these results, we suggest that an increase in task experience (and associated reductions in arousal) uncover modulations in pupil size asymmetries related to attentional processing that are not observable for typical arousal levels. We suggest that these modulations could be a result of right-lateralized attentional processing in the brain that in turn influences structures involved in the control of pupil sizes such as the locus coeruleus. We can exclude a number of possible alternative explanations for this effect related to our experimental setup. Yet, given the novelty of this finding and the arguably speculative explanation of the underlying mechanisms, we suggest that future studies are needed to replicate the present effect and further investigate the underlying mechanisms.

neuroscience↗