Quentin Geissmann

Aarhus University | AU · Center for Quantitative Genetics and Genomics,

In the face of severe environmental crises that threaten insect biodiversity, new technologies are imperative to monitor both the identity and ecology of insect species. Traditionally, insect surveys rely on manual collection of traps, which provide abundance data but mask the large intra- and interday variations in insect activity, an important fa...

During sleep, most animal species enter a state of reduced consciousness characterized by a marked sensory disconnect. Yet some processing of the external world must remain intact, given that a sleeping animal can be awoken by intense stimuli (for example, a loud noise or a bright light) or by soft but qualitatively salient stimuli (for example, th...

Circadian clocks are paramount to insect survival and drive many aspects of their physiology and behaviour. While insect circadian behaviours have been extensively studied in the laboratory, their circadian activity within natural settings is poorly understood. The study of circadian activity necessitates measuring biological variables (e.g., locom...

Maintaining microbiome structure is critical for the health of both plants and animals. By re-screening a collection of Arabidopsis mutants affecting root immunity and hormone crosstalk, we identified a FERONIA (FER) receptor kinase mutant (fer-8) with a rhizosphere microbiome enriched in Pseudomonas fluorescens without phylum-level dysbiosis. Usin...

Maintaining microbiome structure is critical for the health of both plants ¹ and animals ² . In plants, enrichment of beneficial bacteria is associated with advantageous outcomes including protection from biotic and abiotic stress 3,4 . However, the genetic and molecular mechanisms by which plants enrich for specific beneficial microbes without gen...

Sleep appears to be a universally conserved phenomenon among the animal kingdom, but whether this notable evolutionary conservation underlies a basic vital function is still an open question. Using a machine learning–based video-tracking technology, we conducted a detailed high-throughput analysis of sleep in the fruit fly Drosophila melanogaster ,...

The recent development of automatised methods to score various behaviours on a large number of animals provides biologists with an unprecedented set of tools to decipher these complex phenotypes. Analysing such data comes with several challenges that are largely shared across acquisition platform and paradigms. Here, we present rethomics, a set of...

Sleep appears to be a universally conserved phenomenon among the animal kingdom but whether this striking evolutionary conservation underlies a basic vital function is still an open question. Using novel technologies, we conducted an unprecedentedly detailed high-throughput analysis of sleep in the fruit fly Drosophila melanogaster, coupled with a...

The recent development of automatised methods to score various behaviours on a large number of animals provides biologists with an unprecedented set of tools to decipher these complex phenotypes. Analysing such data comes with several challenges that are largely shared across acquisition platform and paradigms. Here, we present rethomics, a set of...

Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able t...

Details of all statistical comparisons. A text file containing the statistical details of all statistical comparisons.

ELife digest Humans spend one-third of their lifetime sleeping, but why we (and other animals) need to sleep remains an unresolved mystery of biology. Our desire to sleep changes depending on how much sleep we’ve already had. If we’ve had a long nap during the day, we may find it harder to fall asleep at night; conversely, if we stay up all night p...

We present ethoscopes, machines for high-throughput ethomics in Drosophila and other animals. Ethoscopes present four unique features: they provide a software and hardware solution that is reproducible and easily scalable; they perform not just real-time tracking, but faithful real-time profiling of behaviour using a supervised machine learning alg...

Motivation: Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system's moments a...

Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the...

Within and between species, multigene families (MF) are known to be highly diverse in terms of both Copy Number Variation (CNV) and allelic diversity. Accordingly, within and between population diversities of MF have a strong potential to result from, or to fuel, local adaptation – and possibly speciation. However, these diversities have seldom bee...

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate...