Biology subjects

Hartasanchez, D. A.

Publications and source records attributed to Hartasanchez, D. A..

4 recordsLinked to original sources

bioRxiv2024

Highly expressed cell wall genes contribute to robustness of sepal size

Reproducibility in organ size and shape is a fascinating trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. Taking the sepal of Arabidopsis as a model, we investigated whether variability of gene expression plays a role in variation of organ size and shape. Previous work from our team identified cell-wall related genes as being enriched among the genes whose expression is highly variable. We then hypothesized that the variation of measured morphological parameters in cell-wall related single knockout mutants could be correlated with the variation in gene expression of the corresponding gene (the knocked-out gene) in wild-type plants. We analyzed sepal size and shape from 16 cell-wall mutants and found that sepal size variability correlates positively, not with gene expression variation, but with mean gene expression of the corresponding gene in wild type. These findings support a contribution of cell-wall related genes to the robustness of sepal size.

plant biology↗

bioRxiv2024

Ongoing hybridisation among clownfishes: the genomic architecture of the Kimbe Bay hybrid zone

Hybrid zones - locations where genetically distinct lineages interact and reproduce - are remarkable resources for exploring the evolutionary trajectory of species. Not only can we learn from hybrid zones about the mechanisms of speciation and how reproductive isolation is maintained, but we can also study their impact on evolutionary processes. Thanks to the advent of next-generation sequencing, we are now able to gain new insight into the structure of hybrid genomes and the factors influencing the outcome of hybridisation. Here, we focus on the Kimbe Bay hybrid zone, a narrow region in the Pacific Ocean where two species of clownfish - Amphiprion chrysopterus and A. sandaracinos - hybridise and give rise to the hybrid A. leucokranos. Based on whole-genome sequencing, we found that the hybrid zone is mainly composed of first-generation hybrids, the first evidence of F2 hybrids in the wild and early backcrosses with A. sandaracinos. The recurrent backcrossing with one of the parental species might lead to adaptive introgression, with few adaptive introgressed loci from A. chrysopterus integrated into the A. sandaracinos genomic background. This study builds upon the growing literature body relative to the evolutionary outcomes of hybridisation and its importance in the evolution of many species.

evolutionary biology↗

bioRxiv2023

Mammalian protein-coding genes exhibit widespread beneficial mutations that are not adaptive

Mutations can be beneficial by bringing innovation to their bearer, allowing them to adapt to environmental change. These mutations are typically unpredictable since they respond to an unforeseen change in the environment. However, mutations can also be beneficial because they are simply restoring a state of higher fitness that was lost due to genetic drift in a stable environment. In contrast to adaptive mutations, these beneficial non-adaptive mutations can be predicted if the underlying fitness landscape is stable and known. The contribution of such non-adaptive mutations to molecular evolution has been widely neglected mainly because their detection is very challenging. We have here reconstructed protein-coding-gene fitness landscapes shared between mammals, using mutation-selection models and a multi-species alignments across 87 mammals. These fitness landscapes have allowed us to predict the fitness effect of polymorphisms found in 28 mammalian populations. Using methods that quantify selection at the population level, we have confirmed that beneficial non-adaptive mutations are indeed positively selected in extant populations. Our work confirms that deleterious substitutions are accumulating in mammals and are being reverted, generating a balance in which genomes are damaged and restored simultaneously at different loci. We observe that beneficial non-adaptive mutations represent between 15% and 45% of all beneficial mutations in 24 of 28 populations analyzed, suggesting that a substantial part of ongoing positive selection is not driven solely by adaptation to environmental change in mammals. Significance statementThe extent to which adaptation to changing environments is shaping genomes is a central question in molecular evolution. To quantify the rate of adaptation, population geneticists have typically used signatures of positive selection. However, mutations restoring an ancestral state of higher fitness lost by genetic drift are also positively selected, but they do not respond to a change in the environment. In this study, we have managed to distinguish beneficial mutations that are due to changing environments and those that are restoring pre-existing functions in mammals. We show that a substantial proportion of beneficial mutations cannot be interpreted as adaptive.

evolutionary biology↗

bioRxiv2022

Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall

Control of organ morphology is a fundamental feature of living organisms. There is, however, observable variation in organ size and shape within a given genotype. Taking the sepal of Arabidopsis as a model, we investigated whether we can use variability of gene expression alongside variability of organ morphology to identify gene regulatory networks potentially involved in organ size and shape determination. We produced a dataset composed of morphological parameters and genome-wide transcriptome obtained from 27 individual sepals from wild-type plants with nearly identical genetic backgrounds, environment, and developmental stage. Sepals exhibited appreciable variability in both morphology and transcriptome, with response to stimulus genes and cell-wall related genes displaying high variability in expression. We additionally identified five modules of co-expressed genes which correlated significantly with morphology, revealing biologically relevant gene regulatory networks. Interestingly, cell-wall related genes were overrepresented in two of the top three modules. Overall, our work highlights the benefit of using coupled variation in gene expression and phenotype in wild-type plants to shed light on the mechanisms underlying organ size and shape determination. Although causality between gene expression and sepal morphology has not been established, our approach opens the way to informed analysis for mutant characterization and functional studies.

plant biology↗