Biology subjects

Roux, C.

Publications and source records attributed to Roux, C..

25 records · Page 2Linked to original sources

bioRxiv2020

Convergent morphology and divergent phenology: unravelling the coexistence of mimetic Morpho butterfly species

The emergence and persistence of closely-related species in sympatry is puzzling because the potential gene flow and the common local selective pressures may lead to either merging or competitive exclusion. Some species of Morpho butterflies occurring in sympatry display highly similar wing colour patterns. Associated with erratic flight abilities, their bright colouration may limit predator success and discourage future attacks. The evolution of similar colouration in sympatric species is thus likely under local selection by predators (i.e. escape mimicry). Such phenotypic similarity may promote interspecific territoriality and/or reproductive interference, questioning how closely-related co-mimetic species become sexually isolated and coexist in sympatry. We performed a series of field experiments using flying Morpho dummies placed in a natural habitat where wild males commonly patrol. Analysing the interactions of wild Morpho with different dummies, we show that similarity in wing colour pattern leads to interspecific territoriality and courtship among sympatric species. Using genomic data, we then showed that sympatric Morpho species are surprisingly strictly isolated despite their close relatedness and the observed heterospecific interactions. Finally, using a mark-recapture experiment, we discovered a strong temporal segregation in patrolling activity of males from two co-mimetic sister species. Such divergence in phenology may favour sympatry between closely-related species, despite behavioural interferences induced by the local convergence in colour pattern. Altogether, our findings show that temporal segregation may facilitate the co-existence of closely-related species sharing the same ecological niche, suggesting that phenological shifts may represent an overlooked factor of sympatric speciation. Our study therefore highlights how the evolution of multiple traits may favour species diversification in sympatry by partitioning niche in different dimensions.

evolutionary biology↗

bioRxiv2020

A new rat model of creatine transporter deficiency reveals behavioral disorder and altered brain metabolism

Creatine is an organic compound used as fast phosphate energy buffer to recycle ATP, important in tissues with high energy demand such as muscle or brain. Creatine is taken from the diet or endogenously synthetized by the enzymes AGAT and GAMT, and specifically taken up by the transporter SLC6A8. Deficit in the endogenous synthesis or in the transport leads to Cerebral Creatine Deficiency Syndromes (CCDS). CCDS are characterized by brain creatine deficiency, intellectual disability with severe speech delay, behavioral troubles such as attention deficits and/or autistic features, and epilepsy. Among CCDS, the X-linked creatine transporter deficiency (CTD) is the most prevalent with no efficient treatment so far. Different mouse models of CTD were generated by doing long deletions in the Slc6a8 gene showing reduced brain creatine and cognitive deficiencies or impaired motor function. We present a new knock-in (KI) rat model of CTD holding an identical point mutation found in patients with reported lack of transporter activity. KI males showed brain creatine deficiency, increased urinary creatine/creatinine ratio, cognitive deficiency and autistic features. Slc6a8xY389C KI rat fairly enriches the spectrum of CTD models and provides new data about the pathology, being the first animal model of CTD carrying a point mutation.

pathology↗

bioRxiv2020

DILS : Demographic Inferences with Linked Selection by using ABC

We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population datasets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, 2) the best genomic model to determine whether the effective size Ne and migration rate N.m are heterogeneously distributed along the genome (implying linked selection) and 3) loci in genomic regions most associated with barriers to gene flow. Also available via a web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations, and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.

evolutionary biology↗

bioRxiv2019

Evaluation of Upconverting nanoparticles towards heart theranostics

Restricted and controlled drug delivery to the heart remains a challenge giving frequent off-target effects as well as limited retention of drugs in the heart. There is a need to develop and optimize tools to allow for improved design of drug candidates for treatment of heart diseases. Over the last decade, novel drug platforms and nanomaterials were designed to confine bioactive materials to the heart. Yet, the research remains in its infancy, not only in the development of tools but also in the understanding of effects of these materials on cardiac function and tissue integrity. Upconverting nanoparticles are nanomaterials that recently accelerated interest in theranostic nanomedicine technologies. Their unique photophysical properties allow for sensitive in vivo imaging that can be combined with spatio-temporal control for targeted release of encapsulated drugs.\n\nHere we synthesized upconverting NaYF4:Yb,Tm nanoparticles and show for the first time their innocuity in the heart, when injected in the myocardium or in the pericardial space in mice. Nanoparticle retention and upconversion in the cardiac region did not alter heart rate variability, nor cardiac function as determined over a 15-day time course ensuing the sole injection. Altogether, our nanoparticles show innocuity primarily in the pericardial region and can be safely used for controlled spatiotemporal drug delivery.\n\nOur results support the use of upconverting nanoparticles as potential theranostics tools overcoming some of the key limitations associated with conventional experimental cardiology.

biophysics↗

bioRxiv2019

ExpressWeb: A Web application for clustering and visualization of expression data.

The recent explosion of transcriptomics and proteomic data have resulted in vast amounts of datasets without connection and sometime too large to be easily analysed. Integration between datasets and analysis of an extracted datasets are limiting factors which need to be solved in order to make full use of the data and to connect data.\n\nExpressWeb is an online web tool that combines a Taylor clustering of expressed data sets to extract gene network with gene annotations to visualise the co-expression network. Data sets can become from personal or publically experiments. ExpressWeb allows to easily compute clustering on expression data and provides friendly and useful visualisation tools as heatmaps, graphs and networks, generating output images which can be used for scientific publications.

bioinformatics↗

bioRxiv2018

Assessing the impact of high-throughput sequencing strategy and model complexity on ABC-inferred demographic history in mussels

Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the joint site frequency spectrum, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e. periodic connectivity) and across genes (i.e. genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding site frequency spectrum, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

evolutionary biology↗

bioRxiv2017

Codon usage bias in animals: disentangling the effects of natural selection, effective population size and GC-biased gene conversion

Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. Codon usage bias in animals has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 31 non-model species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analysing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons are generally preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT{leftrightarrow}GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

evolutionary biology↗