Biology subjects

Betancourt, A.

Publications and source records attributed to Betancourt, A..

9 recordsLinked to original sources

bioRxiv2026

Parallel evolution of industrial melanism in the peppered moth: one locus, many alleles

The extent to which adaptation to environmental change occurs via single or multiple advantageous mutations remains an open question, which we examined by studying the spread of melanic forms of the peppered moth in Britain and continental Europe, in response to industrial coal pollution. In Britain, the darkest melanic form is due to the insertion of a transposable element (carb-TE) into a genomic region called ivory. Here, we characterize the spread of melanic forms in continental Europe from historical records and uncover the genetic basis of European melanism using genomic analyses of modern and museum specimens. We show that European melanism is also associated with variants at ivory, but with multiple alleles featuring structural variants, including several transposable elements, though not carb-TE. The primary central European melanic allele is a genetically dominant 805 base pair deletion (sollichau). Interestingly, melanic individuals with either sollichau (deletion) or carb-TE (insertion) alleles show elevated expression of ivory and its effector micro-RNA (mir-193) compared to non-melanic (typica) individuals, suggesting that contrasting structural variants in ivory have similar regulatory effects. A functional role for sollichau was corroborated, serendipitously, by its presence in a typica individual which also contains a linked deletion of mir-193, which is predicted to cancel the melanizing effect of the sollichau deletion. Our results support the idea that there can be many genetic origins of the same adaptive trait within a species, particularly one with a large effective population size and heterogeneous natural habitat, and when many mutations can give rise to the same phenotype.

evolutionary biology↗

bioRxiv2025

Manifold properties in the macaque medial premotor cortex during switching from attending to tapping to a metronome

Animals synchronize their movements with external rhythms to coordinate perception and action, but the neural population mechanisms that allow them to attend and then initiate and sustain these rhythms remain unclear. Using high-density recordings from the medial premotor cortex (MPC) of two macaque monkeys, we investigated neural dynamics during an attend-then-synchronize tapping task with visual metronomes. We found low-dimensional neural manifolds that capture neural population trajectories. During the attention phase, trajectories exhibited increasing amplitude and oscillatory modulation along successive stimuli, consistent with a resonant-like mechanism. Transition to tapping was marked by a reliable shift into a distinct manifold subspace, enabling accurate decoding of the switch in behavior. In addition, large amplitude and oscillatory indices were higher in successful tapping synchronization trials than in incorrect ones. These findings demonstrate that macaque MPC activity evolves along smooth, low-dimensional trajectories whose geometry governs different perceptual and motor aspects of tapping synchronization.

animal behavior and cognition↗

bioRxiv2025

Leaving Academia: Insights from Evolutionary Biologists on Their Career Transitions and Job Satisfaction

Many who have obtained PhDs in evolutionary biology will ultimately pursue careers that fall outside a narrow definition of an academic career. At the same time, PhD students and supervisors of PhD students are often ill-informed about career options outside of academia. Here, we report on a survey of evolutionary biologists who have pursued non-academic careers, to understand what careers they pursue, how they transitioned into those careers, how well prepared they were, and how satisfied they are with their current work. Overall, the message from this survey is positive- evolutionary biologists are readily employable outside of academia, generally well-prepared for those jobs, and report high levels of satisfaction in their non-academic careers. We also highlight areas where preparation for non-academic careers could be improved, which might be addressed by individual mentors or PhD training programmes.

evolutionary biology↗

bioRxiv2025

The efficacy and accuracy of ribosomal RNA depletion methods

The depletion of ribosomal RNA (rRNA) is a critical step in RNA-sequence analyses, used to enhance the detection of non-rRNA molecules, such as messenger RNAs and non-coding RNAs. However, the efficiency and potential biases introduced by different rRNA depletion methods remain poorly characterized. Here, we evaluated three commercially available rRNA depletion kits - QIAseq FastSelect, riboPOOL, Zymo-Seq RiboFree - for their performance with the parasitic nematode Strongyloides ratti. We assessed the kits efficiency in rRNA removal, the recovery of expressed genes and transposable elements, and the detection of spliced leader sequences and genes operonic organization. Zymo-Seq demonstrated the highest sensitivity and minimal bias in a measure of gene expression, while QIAseq showed the least rRNA depletion and significant differential expression biases. Our findings underscore the importance of empirical validation of rRNA depletion methods, particularly for parasites and non-model organisms, and we suggest that Zymo-Seq as the optimal choice for S. ratti and related nematodes.

genomics↗

bioRxiv2023

Different time encoding strategies within the medial premotor areas of the primate

The measurement of time in the subsecond scale is critical for many sophisticated behaviors, yet its neural underpinnings are largely unknown. Recent neurophysiological experiments from our laboratory have shown that the neural activity in the medial premotor areas (MPC) of macaques can represent different aspects of temporal processing. During interval categorization, we found that preSMA encodes a subjective category limit by reaching a peak of activity at a time that divides the set of test intervals into short and long. We also observed neural signals associated with the category selected by the subjects and the reward outcomes of the perceptual decision. On the other hand, we have studied the behavioral and neurophysiological basis of rhythmic timing. First, we have shown in different tapping tasks that macaques are able to produce predictively and accurately intervals that are cued by auditory or visual metronomes or when intervals are produced internally without sensory guidance. In addition, we found that the rhythmic timing mechanism in MPC is governed by different layers of neural clocks. Next, the instantaneous activity of single cells shows ramping activity that encode the elapsed or remaining time for a tapping movement. In addition, we found MPC neurons that build neural sequences, forming dynamic patterns of activation that flexibly cover all the produced interval depending on the tapping tempo. This rhythmic neural clock resets on every interval providing an internal representation of pulse. Furthermore, the MPC cells show mixed selectivity, encoding not only elapsed time, but also the tempo of the tapping and the serial order element in the rhythmic sequence. Hence, MPC can map different task parameters, including the passage of time, using different cell populations. Finally, the projection of the time varying activity of MPC hundreds of cells into a low dimensional state space showed circular neural trajectories whose geometry represent the internal pulse and the tapping tempo. Overall, these findings support the notion that MPC is part of the core timing mechanism for both single interval and rhythmic timing, using neural clocks with different encoding principles, probably to flexibly encode and mix the timing representation with other task parameters.

neuroscience↗

bioRxiv2022

Premotor population dynamics as neural substrate for auditory and visual rhythmic entrainment

The neural substrate for beat extraction and response entrainment to auditory and visual rhythms is still unknown. Here we analyzed the population activity of hundreds of medial premotor neurons of monkeys performing an isochronous tapping guided by brief flashing stimuli or auditory tones. The animals showed a strong bias towards visual than auditory metronomes, with rhythmic tapping that was more precise and accurate on the former. The population dynamics shared the following properties across modalities: the circular dynamics of the neural trajectories formed a regenerating loop for every produced interval; the trajectories converged in similar state space at tapping times resetting the clock; the tempo of the synchronized tapping was encoded in the trajectories by a combination of amplitude modulation and temporal scaling. In addition, the modality induced a displacement in the neural trajectories in auditory and visual subspaces without greatly altering time keeping mechanism. These results suggest that the interaction between the MPC amodal internal representation of pulse and a modality specific external input generates a neural rhythmic clock whose dynamics governs rhythmic tapping execution across senses.

neuroscience↗

bioRxiv2018

The amplitude in periodic neural state trajectories underlies the tempo of rhythmic tapping

Our motor commands can be exquisitely timed according to the demands of the environment, and the ability to generate rhythms of different tempos is a hallmark of musical cognition. Yet, the neuronal basis behind rhythmic tapping remains elusive. Here we found that the activity of hundreds of primate MPC neurons show a strong periodic pattern that becomes evident when their activity is projected into a lower dimensional state space. We show that different tempos are encoded by circular trajectories that travelled at a constant speed but with different radii, and that this neuronal code is highly resilient to the number of participating neurons. Crucially, the changes in the amplitude of the oscillatory dynamics in neuronal state space are a signature of beat-based timing, regardless of whether it is guided by an external metronome or is internally controlled and is not the result of repetitive motor commands. Furthermore, the increase in amplitude and variability of the neural trajectories accounted for the scalar property of interval timing. In addition, we found that the interval-dependent increments in the radius of periodic neural trajectories are the result of larger number of neurons engaged in the production of longer intervals. Our results support the notion that beat-based timing during rhythmic behaviors is encoded in the radial curvature of periodic MPC neural population trajectories.

neuroscience↗

bioRxiv2018

Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

evolutionary biology↗

bioRxiv2018

Extensive horizontal exchange of transposable elements in the Drosophila pseudoobscura group

While the horizontal transfer of a parasitic element can be a potentially catastrophic, it is increasingly recognized as a common occurrence. The horizontal exchange, or lack of exchange, of TE content between species results in different levels of divergence among a species group in the mobile component of their genomes. Here, we examine differences in the TE content of the Drosophila pseudoobscura species group. We identify several putative horizontal transfer events, and examine the role that horizontal transfer plays in the spread of TE families to new species and the homogenization of TE content in these species. Despite rampant exchange of TE families between species, we find that both TE content differs hugely across the group, likely due to differing activity of each TE family and differing suppression of TEs due to divergence in Y chromosome size, and its resulting effects of TE regulation. Overall, we show that TE content is highly dynamic in this species group, and that it plays a large role in shaping the differences seen between species.\n\nData availabilityAll data used in this study (summarized in table S1) is freely available online through the NCBI short read archive (NCBI SRA: ERR127385, SRR330416, SRR330418, SRR1925723, SRR330426, SRR330420, SRR330423, SRR617430-74). All genomes used are either available through Flybase.org or Popoolation.at.

genomics↗