Biology subjects

Ruggiero, R.

Publications and source records attributed to Ruggiero, R..

3 recordsLinked to original sources

bioRxiv2020

Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

BackgroundThe interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). ResultsWe observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation.. ConclusionsWe demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle the effects of these processes.

genomics↗

bioRxiv2019

Better ears with eyes open: effects of multisensory stimulation with nonconscious visual stimuli on auditory learning

Audiovisual integration may improve unisensory perceptual performance and learning. Interestingly, this integration may occur even when one of the sensory modalities is not conscious to the subject, e.g., semantic auditory information may impact nonconscious visual perception. Studies have shown that the flow of nonconscious visual information is mostly restricted to early cortical processing, without reaching higher-order areas such as the parieto-frontal network. Thus, because multisensory cortical interactions may already occur in early stages of processing, we hypothesized that nonconscious visual stimulation might facilitate auditory pitch learning. In this study we used a pitch learning paradigm, in which individuals had to identify six pitches in a scale with constant intervals of 50 cents. Subjects were assigned to one of three training groups: the test group (Auditory + congruent unconscious visual, AV), and two control groups (Auditory only, A, and Auditory + incongruent unconscious visual, AVi). Auditory-only tests were done before and after training in all groups. Electroencephalography (EEG) was recorded throughout the experiment. Results show that the test group (AV, with congruent nonconscious visual stimuli) performed better during the training, and showed a greater improvement from pre-to post-test. Control groups did not differ from one another. Changes in the AV group were mainly due to performances in the first and last pitches of the scale. We also observed consistent EEG patterns associated with this performance improvement in the AV group, especially maintenance of higher theta-band power after training in central and temporal areas, and stronger theta-band synchrony between visual and auditory cortices. Therefore, we show that nonconscious multisensory interactions are powerful enough to boost auditory perceptual learning, and that increased functional connectivity between early visual and auditory cortices after training might play a role in this effect. Moreover, we provide a methodological contribution for future studies on auditory perceptual learning, particularly those applied to relative and absolute pitch training.

neuroscience↗

bioRxiv2018

Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensis

Gaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Previous studies have been limited to a small number of model species, mostly mammals, and no studies have investigated genomic variation in non avian reptiles. Here we present the first population genomics survey using whole genome re sequencing in the green anole (Anolis carolinensis). This species has emerged as a model for the study of genomic evolution in squamates. We quantified how demography, recombination and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anoles populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the combined effect of background selection and recombination rates is the main contributor to the genomic landscape of differentiation in the anole genome. We further demonstrate that recombination rates are positively correlated with GC content at third codon position (GC3) and confirm the importance of biased gene conversion in shaping genome wide patterns of diversity in reptiles.

evolutionary biology↗