Biology subjects

Caballero, A.

Publications and source records attributed to Caballero, A..

11 recordsLinked to original sources

bioRxiv2026

Estimation of effective size of large continuously distributed populations

Estimation of the effective size (Ne) of large populations with a continuous distribution across wide geographic areas and limited dispersal of individuals has been elusive so far. Estimates of the contemporary Ne from genetic markers for such large, structured populations, typically of plant and marine species, tend to be strongly biased downwards, which has led to question their relevance. Here we show that a recently proposed estimation method of Ne from linkage disequilibrium between markers, which accounts for population structure, yields estimates of metapopulation Ne when the sampling area is sufficiently large. The method is applied to empirical data of maritime pine (Pinus pinaster Aiton). While previous estimates of Ne in pine populations were of the order of a few hundred individuals, we show that estimates of the metapopulation Ne can reach values of the order of tens of thousands of individuals. This result is especially relevant from a conservation point of view, as populations with Ne lower than 500 individuals are considered to be under the risk of extinction.

genetics↗

bioRxiv2025

The ecological dynamics and consequences of phytoplasma in a spring ephemeral

Ecologists have long sought to link within-population dynamics to patterns of species occurrence and persistence across the range. Theoretical models suggest pathogens have important implications for plant populations and perhaps even limit plant distributions, though more empirical evidence is needed, especially in wild plant populations. In the field, we characterized the infection dynamics of phytoplasma, a vectored and sterilizing bacterial pathogen, in wild populations of white trillium. We identified the highest molecular matches for the local bacterial strain and putative vectors. We then leveraged iNaturalist data to reveal patterns and potential drivers of phytoplasma occurrence across the range of white trillium. Within populations, we found that phytoplasma symptoms were more likely in low host density plots, where insects occupied a higher proportion of trillium, indicative of an encounter-dilution effect. Leafhoppers in the genus Empoasca were positive for phytoplasma, suggesting they are a candidate vector of disease between trilliums at our field site. The closest match to our local phytoplasma was related to Candidatus Phytoplasma pruni, ribosomal group 16SrIII-F. Phytoplasma symptoms were widely distributed across trilliums range, even at range edges, and probability of symptoms was significantly increased by proximity to cropland. We studied the impacts of a sterilizing, vector-transmitted pathogen on host plant populations and patterns of infection across host range. Our results suggest sap-feeding insects do not occupy all hosts at high host densities, thereby reducing transmission and leading to higher likelihood of finding infection at low host densities, and a higher proportion of host plants infected at low host densities. At a range-wide scale, we found evidence that the pathogen was able to persist across both the core and edge of host ranges. Thus, negative-density dependent sterilizing pathogens may challenge host populations across the range.

ecology↗

bioRxiv2025

KLinterSel: Intersection among candidates of different selective sweep detection methods

Detecting signals of natural selection, including selective sweeps, in genomic data often involves applying several methods in parallel. Regions identified by multiple approaches are usually considered strong candidates, as agreement among methods is often taken as supporting evidence. However, the extent to which such overlaps exceed random expectations is rarely evaluated formally. When genomic elements are not independent, coincident candidate sites may arise from the underlying structure of the data rather than from genuine methodological concordance. To address this problem, we introduce two complementary statistical tests designed to evaluate whether the observed overlap among candidate sites detected by different methods exceeds what would be expected by chance. The first is a fast parametric test based on a sequentially conditioned hypergeometric framework that evaluates k-way intersections among candidate sets across genomic windows. The second relies on Monte Carlo simulations and compares the observed inter-method distance profiles with those expected under random association, taking into account the empirical distribution of SNPs along the genome. By capturing different aspects of concordance, these approaches allow agreement among methods to be assessed across multiple spatial scales. Both tests are implemented in the program KLinterSel, which also identifies clusters of candidate sites detected by different selection-detection methods within a user-defined distance threshold. We illustrate its application using candidate loci associated with resistance of the common cockle (Cerastoderma edule) to the parasite Marteilia cochillia. The software is written in Python and is available on GitHub together with documentation and precompiled executables for major operating systems.

genomics↗

bioRxiv2024

Harnessing homeostatically active RhoC at cell junctions preserves human endothelial barrier function during inflammation

Rho GTPases are molecular targets of bacterial toxins that modulate their enzymatic activity. RhoA, RhoB and RhoC are almost identical and play critical roles in generating actomyosin-mediated contractile forces that cause endothelial hyperpermeability during inflammation. Searching for new treatments to modulate endothelial integrity, we demonstrate that the specific and simultaneous activation of these three Rho GTPases with a chimeric recombinant toxin does not induce cell contraction but enhances homeostatic endothelial barrier function, increases reticular adherens junctions and preserves the microvascular endothelium in response to pathological inflammatory challenges in vitro and in vivo. This pro-barrier effect is specifically mediated by RhoC, whose activity is increased by cell confluence. The uniqueness of RhoC relies on an arginine 188 within its hypervariable region that determines its junctional localization, high homeostatic activity, and barrier-protective function. Quantitative proteomics revealed that RhoC regulates the expression of myosin light chain proteins and junction-stabilizing actomyosin. Thus, harnessing the activity of RhoC represents a potential therapy for strengthening endothelial barriers during pathological inflammation.

cell biology↗

bioRxiv2022

Specific sensory neurons and insulin-like peptides modulate food type-dependent oogenesis and fertilization in Caenorhabditis elegans

AbstractAn animals responses to environmental cues are critical for its reproductive program. Thus, a mechanism that allows the animal to sense and adjust to its environment should make for a more efficient reproductive physiology. Here we demonstrate that in Caenorhabditis elegans specific sensory neurons influence onset of oogenesis through insulin signaling in response to food-derived cues. The chemosensory neurons ASJ modulate oogenesis onset through the insulin-like peptide (ILP) INS-6. In contrast, other sensory neurons, the olfactory neurons AWA, regulate food type-dependent differences in C. elegans fertilization rates, but not onset of oogenesis. AWA modulates fertilization rates at least partly in parallel to insulin receptor signaling, since the insulin receptor DAF-2 regulates fertilization independently of food type, which requires ILPs other than INS-6. Together our findings suggest that optimal reproduction requires the integration of diverse food-derived inputs through multiple neuronal signals acting on the C. elegans germline.

developmental biology↗

bioRxiv2021

Loss of Depalmitoylation Exaggerates Synaptic Upscaling and Leads to Neuroinflammation in a Lysosomal Storage Disease

Palmitoylation and depalmitoylation are the dichotomic processes of lipid modification regulating protein trafficking, recycling, and degradation, thereby controlling proteostasis. Despite our understanding of palmitoylation, depalmitoylation is far less studied. Here, we study a lysosomal depalmitoylating enzyme, palmitoyl-protein thioesterase 1 (PPT1), associated with the devastating neurodegenerative condition CLN1 disease and show that dark-rearing Ppt1-/- mice, which induces synaptic upscaling in vivo, worsen the symptoms. In Ppt1-/- cortical neurons, upscaling induction triggers exaggerated responses of synaptic calcium-permeable AMPA receptors composed of palmitoylated GluA1 subunits. Consequently, Ppt1-/- visual cortex exhibits hypersynchrony in vivo. Remarkably, we also find an overload of palmitoylated A-kinase anchor protein 5 (Akap5) in Ppt1-/- mouse brains, leading to microglial activation through NFAT. These findings indicate Ppt1 acts as a gatekeeper of homeostatic plasticity by regulating the proteostasis of palmitoylated synaptic proteins. Moreover, our results suggest that perturbed depalmitoylation results in neuroinflammation, which is common to neurodegenerative diseases.

neuroscience↗

bioRxiv2021

Natural selection does not affect the estimates of effective population size based on linkage disequilibrium

The effective population size (Ne) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in Ne across time using measures of genome diversity or linkage disequilibrium between markers. Selection is expected to reduce diversity and Ne, and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and of recombination rate heterogeneity in the estimation of historical Ne. We also investigate the relationship between diversity parameters and Ne across the different regions of the genome using human marker data. We show that the estimates of historical Ne obtained from linkage disequilibrium between markers (NeLD) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, what could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of NeLD obtained for particular genomic regions do not correlate with recombination rate, nucleotide diversity, polymorphism, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that NeLD measures are merely indicative of demographic changes in population size across generations. Author summaryThe inference of the demographic history of populations is of great relevance in evolutionary biology. This inference can be made from genomic data using coalescence methods or linkage disequilibrium methods. However, the assessment of these methods is usually made assuming neutrality (absence of selection). Here we show by computer simulations and analyses of human data that the estimates of historical effective population size obtained from linkage disequilibrium between markers are unaffected by natural selection, either positive or negative. In contrast, estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for recent estimations of human demography. Thus, only linkage disequilibrium methods appear to provide unbiased estimates of the population census size.

genetics↗

bioRxiv2021

Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus

The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated subspecies. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of subspecies divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry inference. The transition into agricultural environments has favoured southwestern var. rudis ancestry that leads to higher biomass and environment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation to agricultural habitats independent of ancestry effects, including marginally higher biomass and later flowering in agricultural populations, and a time to germination home advantage. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales--through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.

evolutionary biology↗

bioRxiv2021

Reviewing the consequences of genetic purging on the success of rescue programs

Genetic rescue is increasingly considered a promising and underused conservation strategy to reduce inbreeding depression and restore genetic diversity in endangered populations, but the empirical evidence supporting its application is limited to a few generations. Here we discuss on the light of theory the role of inbreeding depression arising from partially recessive deleterious mutations and of genetic purging as main determinants of the medium to long-term success of rescue programs. This role depends on two main predictions: (1) The inbreeding load hidden in populations with a long stable demography increases with the effective population size; and (2) After a population shrinks, purging tends to remove its (partially) recessive deleterious alleles, a process that is slower but more efficient for large populations than for small ones. We also carry out computer simulations to investigate the impact of genetic purging on the medium to long term success of genetic rescue programs. For some scenarios, it is found that hybrid vigor followed by purging will lead to sustained successful rescue. However, there may be specific situations where the recipient population is so small that it cannot purge the inbreeding load introduced by migrants, which would lead to increased fitness inbreeding depression and extinction risk in the medium to long term. In such cases, the risk is expected to be higher if migrants came from a large non-purged population with high inbreeding load, particularly after the accumulation of the stochastic effects ascribed to repeated occasional migration events. Therefore, under the specific deleterious recessive mutation model considered, we conclude that additional caution should be taken in rescue programs. Unless the endangered population harbors some distinctive genetic singularity whose conservation is a main concern, restoration by continuous stable gene flow should be considered, whenever feasible, as it reduces the extinction risk compared to repeated occasional migration and can also allow recolonization events.

genetics↗

bioRxiv2020

Fibrous caps in atherosclerosis form by Notch-dependent mechanisms shared with arterial media development

RationaleThe rupture of the fibrous cap in atherosclerotic lesions is the underlying cause of most thrombi leading to heart attack and a frequent cause of stroke. Caps are produced by smooth muscle cells (SMCs) that are recruited to the subendothelial space. We hypothesized that the recruitment mechanisms are likely common to embryonic artery development, which relies prominently on Notch signaling to form the subendothelial layers of medial SMCs. ObjectiveTo analyze the causal roles of the Notch signaling pathway in SMCs for atherogenesis and cap formation. Methods and ResultsNotch elements involved in arterial media development were found expressed in regions of fibrous cap in mouse plaques. To assess the causal role of Notch signaling in cap formation, we studied atherosclerosis in mice in which the Notch pathway was inactivated specifically in SMCs by conditional knockout of the essential effector transcription factor RBPJ. No major effects were observed on plaque size, but the presence of cap SMCs was significantly reduced. Lineage tracing revealed that the accumulation of SMC-derived plaque cells in the cap region was unaltered but that Notch-defective cells failed to re-acquire the SMC phenotype in the cap. To analyze whether the accumulation of SMC-derived cells in atherogenesis requires down-regulation of Notch signaling, we studied atherosclerosis in mice with constitutive Notch signaling in SMCs achieved by conditional expression of the Notch intracellular domain. Forced Notch signaling inhibited the ability of medial SMCs to contribute to plaque cells, including both cap SMCs and osteochondrogenic cells, and significantly reduced atherosclerosis development. ConclusionsSequential loss and gain of Notch signaling is needed to build the cap SMC population. The shared mechanisms with embryonic arterial media assembly suggest that the fibrous cap forms as a neo-media that restores the connection between endothelium and stabilizing SMCs, which is transiently disrupted by atherogenesis.

pathology↗

bioRxiv2018

Inferring the nature of missing heritability in human traits

Thousands of genes responsible for many diseases and other common traits in humans have been detected by Genome Wide Association Studies (GWAS) in the last decade. However, candidate causal variants found so far usually explain only a small fraction of the heritability estimated by family data, the rest remaining missing. The most common explanation for this observation is that the missing heritability corresponds to variants, either rare or common, with very small effect, which pass undetected due to a lack of statistical power. We carried out a meta-analysis using data from the NHGRI-EBI GWAS Catalog in order to explore the distribution of gene effects for a set of 59 complex traits, to investigate the factors related to new gene discovery and to quantify their contributions to heritability. With the data obtained we were able to predict the expected distribution of gene effects for 16 traits and diseases including cancer and immune disorders, the missing number of genes yet to be discovered, and the additive contribution of common variants to heritability. Our results indicate that, for most traits, the additive contribution of hundreds or thousands of genes is able to explain the familiar heritability. However, for some traits, the predicted heritability is lower than the familiar one, so that part of the missing heritability cannot be explained by the contribution of common variants with additive effects, and other phenomena (e.g. dominance or epistasis) should be invoked.\n\nAUTHOR SUMMARYThe heritability of biological traits refers to the fraction of the phenotypic (i.e. visible or diagnosable) variability that is explained by the underlying genetic variability. Despite the efforts made to find the genes responsible for complex traits and diseases, most of the heritability explained by the variants found explains only a small fraction of that measured by population and family studies. The remaining missing heritability is usually assumed to be due to the additive effect of undetected variants. Here we carried out a meta-analysis using records from a publicly available database of genome-wide studies on humans. With these data, we were able to investigate and make inferences on the nature of heritability and the factors associated to new gene discovery. Our results indicate that increasing population sample size, as well as its diversity, enhances the discovery of new genes, but these have lower and lower effects, contributing little to heritability. We were also able to predict the distribution of gene effects for many traits and the number of variants needed to fully explain the heritability. For some traits, the additive effects of single variants yet to be discovered cannot explain the heritability, suggesting that other sources of variation are involved.

genetics↗