Biology subjects

Arrufat, P.

Publications and source records attributed to Arrufat, P..

4 recordsLinked to original sources

bioRxiv2025

Universal single-copy genes and 16S rDNA present incongruent evolutionary histories in Vibrio

A common technique for the study of the diversity and evolution of microbial communities is 16S rDNA sequencing. However, high sequence identity and variable copy number constrain the application of 16S rDNA in differentiation of closely related taxa and estimation of species relative abundance in environmental samples. A promising alternative is the use of universal single-copy genes (USCGs) as phylogenetic markers. We develop this by analyzing a set of USCG loci from the genus Vibrio, which holds over 100 species of substantial ecological and epidemiological relevance. The phylogenetic histories of these loci, of representative copies of 16S and 23S rDNA genes, and of a collection of 16S rDNA partial sequences were reconstructed using Bayesian inference. Taxon resolution was assessed according to consensus tree topology and clade credibility values. In addition, the congruence among posterior distributions of phylogenetic estimates of the different loci was calculated using Robinson-Foulds distances and visualized with non-metric multidimensional scaling (NMDS). Phylogenetic analyses reveal that USCG loci produce highly resolved trees in comparison to those of 16S and 23S rDNA sequences. We also observe relatively high congruence among phylogenies of USCG loci while rDNA phylogenies diverge from these. The loci mfd and uvrC are highlighted for further research on Vibrio evolution and analysis of environmental samples. Moreover, possible sources of phylogenetic incongruence between USCG and rDNA loci include differential susceptibility to horizontal gene transfer, as potentially explained by the complexity hypothesis, or lack of phylogenetic information due to limited sequence variability in rDNA sequences.

microbiology↗

bioRxiv2025

Independent colonisations of serpentine habitats highlight species-specific evolutionary histories of lineage diversification

Serpentine soils are characterized by high levels of heavy metals, low nutrient availability, and water scarcity, presenting significant ecological challenges for plant species. Nonetheless, some species have adapted successfully to these conditions. We investigate the population genomic structure, evolutionary history and phenotypic differentiation of three diploid generalist plant species, Lavandula stoechas L., Halimium atriplicifolium (Lam) Spach. subsp. atriplicifolium, and Phlomis purpurea L., all of which inhabit adjacent serpentine and non-serpentine soils in the Malaga region in the southern Iberian Peninsula (Spain). We explore whether populations from serpentine and non-serpentine soils represent distinct evolutionary lineages and whether there is genomic and phenotypic differentiation associated with serpentine conditions. We measured plant height and specific leaf area (SLA) to detect potential ecotypic variation associated with soil type. A ddRADseq SNP dataset was generated for each species, representing 10 populations from serpentine and 10 from non-serpentine soils. We ordinated genotype data to assess genomic variation, conducted an ADMIXTURE analysis to infer ancestral groups, and used Treemix analyses to investigate phylogenetic relationships and gene flow events between populations. Isolation by distance (IBD) analyses evaluated the role of geographic separation in observed genomic differentiation. Our results reveal species-specific patterns of genomic, and to some extent phenotypic, differentiation between serpentine and non-serpentine populations, with evidence of multiple colonisations of serpentine sites in all three species. The study highlights the role of historical differentiation and subsequent gene flow in shaping the genomic structure of plant populations, alongside observed variation in phenotypic traits across environments.

evolutionary biology↗

bioRxiv2024

Cellects, a software to quantify cell expansion and motion

Cellects is a user-friendly and open-source software for automated quantification of biological growth, motion, and morphology from 2D image data and time-lapse sequences (2D + t), acquired under a wide range of experimental conditions and biological systems (from fungal colonies to unicellular branching networks). The software is available as a stand-alone version, featuring a graphical interface that supports interactive parameter tuning, visualization, validation, and batch processing. The analysis pipeline can be extended and customized using a dedicated Python API. The typical inputs and outputs are as follows. Cellects is designed to process grayscale or color images originating from standard microscopy, macroscopic imaging setups, or camera-based platforms. The software supports single or multiple organisms growing or moving in one or several arenas and can analyze multiple folders sequentially. All quantitative results (area, circularity, orientation axes, centroid trajectories, oscillations, network topology...) are exported as standardized .csv files suitable for downstream statistical analysis, ensuring reproducibility and integration into existing workflows.

bioinformatics↗

bioRxiv2017

Investigating termite nest thermodynamics using a quick-look method and the heat equation

Termite mounds are often cited as an example of efficient thermoregulated structures. Nest thermal stability can be critical for insects that are particularly sensitive to heat and desiccation. Few studies have measured internal temperature of termite nests with respect to environmental parameters, especially in Neotropical species. In this study, we analyzed the thermal profiles of different parts of Procornitermes araujoi nests, a neotropical mound-building termite of the Brazilian cerrado. To read into our dataset we first used rasterization, a method that allows a quick-look assessment of time-series. Our results show that nest architecture efficiently buffers against environmental temperature fluctuations while at the same time maintaining a relatively high internal temperature in the core. This rather stable internal climate follows nevertheless the external temperature long-term averages. Using a novel numerical scheme, we further show that the heat transfer dynamics are well described by the classical heat equation, with an additional heat source whose origin is discussed.

ecology↗