Biology subjects

Franco, M.

Publications and source records attributed to Franco, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Stemness overcomes IFNγ-induced antitumour exhaustion in human macrophages

Macrophages hold great promise for antitumour therapies (1-4), particularly owing to their ability to infiltrate solid tumours (5). Yet therapeutic success has been limited (6,7), because macrophages exhibit rapid exhaustion of antitumorigenic activity in the tumour (5,8,9). Here, we induced a stem-like self-renewal programme in human induced pluripotent stem cell (iPSC)-derived macrophages by deleting the self-renewal restricting transcription factors MAFB and MAF (MAF-DKO). Human MAF-DKO macrophages showed activated stem cell signatures, increased clonogenicity and proliferative potential. Increased self-renewal capacity was accompanied by enhanced mitochondrial fitness and invigorated energy metabolism. Importantly, these stemness features prevented exhaustion, cellular aging-associated parameters and loss of energy efficiency that are typically associated with proinflammatory macrophage activation. In addition, activated MAF-DKO macrophages showed a broad loss of IFN{gamma}-triggered immunosuppressive pathways (10,11), induced a super-activated state with robust cytotoxic activity and resisted exhaustion upon tumour cell exposure. Consequently, activated MAF-DKO macrophages showed intratumoral persistence with a stable antitumoral phenotype in vivo, conferred robust reduction of tumour burden and extended survival of tumour-bearing mice. Together, this demonstrates that the induction of stemness in human macrophages can overcome critical roadblocks of antitumour therapy by conferring resistance to activation-triggered exhaustion of antitumour activity in the TME.

immunology↗

bioRxiv2026

Mitochondria-Associated Transcription Precedes Oxidative Phosphorylation Activation During Human Pre-Implantation Embryogenesis

Mitochondria undergo significant structural and functional changes during human pre-implantation embryogenesis, yet the transcriptional activity of both nuclear-encoded mitochondria-associated genes and mitochondrially transcribed genes across this developmental window remains poorly characterized. While mitochondria are established as the primary energy source for the early embryo, emerging evidence suggests they may also influence lineage specification through epigenetic regulation and metabolite availability. To investigate this, we reanalyzed two publicly available human single-cell RNA sequencing datasets filtered for mitochondria-associated genes using the MitoCarta 3.0 reference database, with separate analyses conducted on the nuclear-encoded and mitochondrially transcribed subsets. The first dataset spanned individual blastomeres from the oocyte through blastocyst stage, and the second compared trophectoderm and inner cell mass cells isolated from blastocysts. Mitochondria-associated gene expression was sufficient to cluster human blastomeres by developmental stage, with morula and blastocyst stage cells forming well-defined clusters. Mitochondrially transcribed genes were found to be the primary drivers of clustering in earlier developmental stages, while nuclear-encoded mitochondria-associated genes drove clustering at the blastocyst stage. A pronounced shift in the expression of both gene sets was identified at the transition from the 4-cell to the 8-cell stage, with 115 unique differentially expressed genes identified across the two stages immediately following this transition, compared to only 5 across the two prior stages. The timing of this transcriptional upregulation, preceding the known onset of oxidative phosphorylation at approximately the 32-cell stage, suggests a mitochondrial role in early embryogenesis beyond energy production. Analysis of trophectoderm and inner cell mass cells showed that mitochondrial gene expression profiles partially distinguished these two lineages, consistent with known differences in mitochondrial activity between them. These findings suggest that both nuclear-encoded and mitochondrially transcribed gene expression is upregulated prior to the first lineage specification event in the human embryo, potentially contributing to epigenetic regulation and cell fate determination through altered metabolite availability. A limitation of this study is its reliance on transcriptomic data alone; future work incorporating functional metabolite measurements will be needed to establish causality. Nonetheless, these data reframe mitochondria as active participants in early human developmental programming rather than passive energy suppliers.

developmental biology↗

bioRxiv2026

Positive germline selection of mtDNA mutations: evidence from the oocyte.

Purifying selection is the removal of detrimental mutations. Nuclear DNA mutations are purged by removing mutant individuals, embryos, or germline cells. Because mtDNA is present in numerous copies per cell, purifying selection of mtDNA mutations introduces an additional layer of complexity. The intracellular mutant fraction can change due to clonal expansion/reduction of mutant mtDNA molecules in germline cells. Different research groups have reported either negative (purifying), or positive (destructive) germline mtDNA selection. In this study, we use recently published high-fidelity data on mtDNA mutations in individual human oocytes from the Makova laboratory (Arbeithuber et al., 2025) to resolve this disagreement. To assess selection, we used the "selective expansion" metric St, which compares the average weighted rate of clonal expansion in a set of mutations tested for selection (e.g. non-synonymous mutations) to that of the set of synonymous mutations. We found that, on average, noncoding oocyte mutations in the control region expand faster than synonymous mutations, i.e., are under positive selection. Intriguingly, mutations in the coding region, the detrimental ones in particular, were also on average under positive selection. The prescence of average positive selection does not preclude purifying selection against individual mutations; it only indicates that positive selection dominates in aggregate mutational dynamics. Positive selection impacts the dynamics of de novo germline mutations that arise in primordial germ cells or oocytes and have not yet been inherited by the next generation. Contrastly, mutations that are passed to subsequent generations are under average purifying selection. We suggest that initial positive selection begets subsequent purifying selection by increasing intracellular mutant fractions to levels at which their deleterious effects become phenotypically apparent and can be efficiently removed.

genetics↗

bioRxiv2025

Are mitochondrial DNA mutations under purifying selection in somatic tissues?

The extent to which somatic mitochondrial DNA (mtDNA) mutations are subject to selection is a fundamental question relevant to development, mitochondrial disease, cancer, and aging. Recently a study from the Sudmant laboratory that used an advanced, high fidelity mutational analysis reported that somatic mutations in protein-coding genes exhibit signatures of negative selection. This report came as surprise as several other studies including those that used same technology reported either lack of selection or positive (destructive) selection on somatic mutations. We hypothesized that these discrepancies may stem, in part, from the inclusion of germline mutations in addition to somatic ones, which could bias selection analyses due to the high synonymity of the latter. To test this, we reanalyzed the Sudmant dataset by separating mutations into germline (defined as shared between related animals) and somatic (not shared between tissues of an animal). We then employed a cumulative curve approach to assess selection without bias. Our analysis reveals that, indeed, an apparent purifying selection signal is driven by an admixture of synonymous germline mutations and disappears upon their removal. The remaining somatic mutations for most part show overall dynamics consistent with neutral drift. However, mutations at higher mutant fractions show positive selection trend, most compatible with a low proportion of mutations experiencing positive selection. While we do not exclude rare or context-specific selection events, our results argue against pervasive somatic selection and highlight the importance of rigorous stratification when interpreting mtDNA mutational patterns.

genetics↗

bioRxiv2025

Inhibition of PTCH1 drug efflux activity enhances chemotherapy efficacy against triple negative breast cancer

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subgroup characterized by a high risk of resistance to chemotherapies and high relapse potential. High levels of mRNA from the Hedgehog receptor PTCH1 are associated with poor prognosis in TNBC. PTCH1 is overexpressed in many aggressive cancers. We previously reported that PTCH1 is a multidrug transporter that triggers resistance to chemotherapy of adrenocortical carcinoma and melanoma cells, and that inhibiting PTCH1 drug efflux strongly enhanced chemotherapy efficacy on these cell lines both in vitro and in vivo. In the present study, we found that PTCH1 inhibition also significantly inhibited doxorubicin efflux in three TNBC cell lines leading to a strong increase of the cytotoxic effect of doxorubicin and docetaxel, and an inhibition of cell migration. Altogether, our data highlight the therapeutic potential of targeting PTCH1 drug efflux activity using drug association strategies for the treatment of TNBC patients.

cancer biology↗

bioRxiv2025

Human mammary 3D spheroid models uncover the role of filopodia in breaching the basement membrane to facilitate invasion

Basement membranes (BM) are thin, nanoporous sheets of specialized extracellular matrix (ECM) that line epithelial tissues. They are dynamic structures that serve multiple key functions, as evidenced by numerous diseases, including cancer progression, that are associated with their alterations. Our understanding of the BM and its communication with adjoining epithelial cells remains highly fragmented due to the BMs complex molecular architecture, the lack of molecular tools, limitations in utilizing high-resolution imaging techniques to BMs assembled on tissues, and the difficulty of assessing their functional contributions in vivo. Here, by combining multiple -omics analyses and advanced microscopy methodologies, we characterized the BM from two normal human mammary epithelial cell lines, MCF10 and HMLE, grown as spheroids in 3D matrices. Our findings indicate that the spheroids autonomously assemble a BM exhibiting all the molecular, structural, and biophysical characteristics of physiological BM. Using these minimalist model systems, we show for the first time that the laminins, perlecan, and the hemidesmosomes are all arranged along a shared porous lattice defined by the collagen IV molecular network. Next, we demonstrate that the invasion-promoting PSD4/EFA6B knockout, found in patients with breast cancer, decreases the expression of BM components and their assembly on the spheroid surface. We then show that invasive spheroids develop enlarged pores in the BM via filopodia-like plasma membrane extensions, which further expand in a protease-dependent manner, thereby facilitating the passage of invasive cells. Significance StatementThe basement membrane (BM) directs epithelial tissue architecture and behavior. How tumor cells breach this barrier during invasion remains poorly understood. Using minimalist 3D spheroid models mimicking physiological BM assembly, we reveal a novel infiltration mechanism. Filopodia-like protrusions perforate and widen BM pores. This facilitates cell dissemination through sequential protease-independent and -dependent steps.

cell biology↗

bioRxiv2025

The genetic architecture of the human bZIP family

Generative biology holds the promise to transform our ability to design and understand living systems by creating novel proteins, pathways, and organisms with tailored functions that address challenges in medicine, sustainability, and technology. However, training generative models requires large quantities of data that captures the genetic architecture of protein function in all its complexity, but these are currently scarce. Here, we systematically mutagenized all 54 human basic-leucine zipper (bZIP) domains and quantified their interactions with each other using bindingPCA, a quantitative deep mutational scanning assay. This resulted in [~]2 million interaction measurements, capturing the effect of all single amino acid substitutions at each of the 35 interfacial positions. We found that mutation effects are largely additive in the vicinity of each wild-type bZIPs, but diverge across the family, indicating strong context dependency. A global additive thermodynamic model provided moderate prediction of mutation effects, while individual models per bZIP achieved higher performance, supporting a model of local simplicity and global complexity. Our results therefore suggest that the genetic architecture of protein function is more complex than previously anticipated, which could hinder predictability. However, a convolutional neural network trained on this dataset could accurately predict binding scores from sequence alone. Furthermore, the model enabled the design of synthetic bZIPs with high target specificity, demonstrating practical applicability for bioengineering purposes. Our study shows that capturing family-wide diversity is essential to reveal context dependencies and train accurate quantitative models of protein-protein interactions.

biophysics↗

bioRxiv2025

Human RAP2A Homolog of the Drosophila Asymmetric Cell Division Regulator Rap2l Targets the Stemness of Glioblastoma Stem Cells

Asymmetric cell division (ACD) is a fundamental process to balance cell proliferation and differentiation during development and in the adult. Cancer stem cells (CSCs), a very small but highly malignant population within many human tumors, are able to provide differentiated progeny by ACD that contribute to the intratumoral heterogeneity, as well as to proliferate without control by symmetric, self-renewing divisions. Thus, ACD dysregulation in CSCs could trigger cancer progression. Here we consistently find low expression levels of RAP2A, the human homolog of the Drosophila ACD regulator Rap2l, in glioblastoma (GBM) patient samples, and observe that scarce levels of RAP2A are associated with poor clinical prognosis in GBM. Additionally, we show that restitution of RAP2A in GBM neurosphere cultures increases the ACD of glioblastoma stem cells (GSCs), decreasing their proliferation and expression of stem cell markers. Our results support that ACD failures in GSCs increases their spread, and that ACD amendment could contribute to reduce the expansion of GBM.

cancer biology↗

bioRxiv2024

In silico biophysics and rheology of blood and red blood cells in Gaucher Disease

Gaucher Disease (GD) is a rare genetic disorder characterized by a deficiency in the enzyme glucocerebrosidase, leading to the accumulation of glucosylceramide in various cells, including red blood cells (RBCs). This accumulation results in altered biomechanical properties and rheological behavior of RBCs, which may play an important role in blood rheology and the development of bone infarcts, avascular necrosis (AVN) and other bone diseases associated with GD. In this study, dissipative particle dynamics (DPD) simulations are employed to investigate the biomechanics and rheology of blood and RBCs in GD under various flow conditions. The model incorporates the unique characteristics of GD RBCs, such as decreased deformability and increased aggregation properties, and aims to capture the resulting changes in RBC biophysics and blood viscosity. This study is the first to explore the Youngs modulus and aggregation parameters of GD RBCs by validating simulations with confocal imaging and experimental RBC disaggregation thresholds. Through in silico simulations, we examine the impact of hematocrit, RBC disaggregation threshold, and cell stiffness on blood viscosity in GD. The results reveal three distinct domains of GD blood viscosity based on shear rate: the aggregation domain, where the RBC disaggregation threshold predominantly influences blood viscosity; the transition area, where both RBC aggregation and stiffness impact on blood viscosity; and the stiffness domain, where the stiffness of RBCs emerges as the primary determinant of blood viscosity. By quantitatively assessing RBC deformability, RBC disaggregation threshold, and blood viscosity in relation to bone disease, we find that the RBC aggregation properties, as well as their deformability and blood viscosity, may contribute to its onset. These findings enhance our understanding of how changes in RBC properties impact on blood viscosity and may affect bone health, offering a partial explanation for the bone complications observed in GD patients. Author summaryIn Gaucher Disease (GD), a genetic deficiency in the enzyme glucocerebrosidase leads to the accumulation of glucosylceramide in red blood cells (RBCs), resulting in altered biomechanical properties. These changes affect blood flow characteristics, particularly blood viscosity, and may contribute to bone health issues seen in GD patients, including bone infarcts, avascular necrosis (AVN), and other bone diseases. In our study, we apply dissipative particle dynamics (DPD) simulations to explore how GD impacts RBC behavior under various flow conditions. We model GD RBCs with decreased deformability and increased aggregation, examining how these properties influence blood viscosity across three distinct shear rate domains: aggregation, transition, and stiffness. By validating our simulations with confocal imaging data and experimental RBC disaggregation thresholds, we quantitatively assess the effects of RBC stiffness, aggregation, and hematocrit levels on blood flow in GD. We find that the RBC aggregation properties, deformability and blood viscosity, may contribute to the onset of bone disease. These findings improve our understanding of how changes in RBC properties influence blood viscosity and may contribute to bone health issues, providing a partial explanation for the bone complications observed in GD patients.

biophysics↗

bioRxiv2024

Evolutionary mismatch between nuclear and mitochondrial genomes does not promote reversion mutations in mtDNA.

Serrano et al. (Serrano et al., 2024) use a high-fidelity somatic mtDNA mutation analysis in conplastic mice in which mtDNA was replaced with exogenous mtDNA of different mouse strains. Serrano reported apparent abundant somatic reversion mutations in the exogenous mtDNA that seemed to restore the original mito-nuclear match. If real, such a phenomenon would have important implications for health and genetics. In todays highly mixed human population, the pairing of potentially mismatched nuclear and mitochondrial genomes is widespread, so the proposed reversion mutagenesis should be commonplace. We demonstrate, however, that these reversion mutations are not real but originate from cross-contamination between samples and from NUMTs, the mtDNA pseudogenes located in the nuclear genome.

bioinformatics↗

bioRxiv2024

Cell sorting based on single nucleotide variation enables characterization of mutation-dependent transcriptome and chromatin states.

Single nucleotide variants (SNVs) contribute to cancer by altering the coding and the non-coding regions of the genome. Connecting SNVs to transcriptomic and epigenetic changes at the single-cell level remains challenging. To enable studies of rare cell populations harboring specific point mutations, we developed STAR-FACS, Specific-To-Allele PCR-FACS, to sort cells based on genomic allele alterations. We show that STAR-FACS can separate cells based on TERT promoter mutation status and is compatible with bulk and single-cell transcriptomic and epigenetic profiling. We demonstrate that glioblastoma cell lines derived from the same tumor but harboring distinct TERT promoter SNVs have different transcriptional programs.

cancer biology↗

bioRxiv2024

Red blood cell passage through deformable interendothelial slits in the spleen: Insights into splenic filtration and hemodynamics

The spleen constantly clears altered red blood cells (RBCs) from the circulation, tuning the balance between RBC formation (erythropoiesis) and removal. The retention and elimination of RBCs occur predominantly in the open circulation of the spleen, where RBCs must cross submicron-wide inter-endothelial slits (IES). Several experimental and computational studies have illustrated the role of IES in filtrating the biomechanically and morphologically altered RBCs based on a rigid wall assumption. However, these studies also reported that when the size of IES is close to the lower end of clinically observed sizes (less than 0.5 m), an unphysiologically large pressure difference across the IES is required to drive the passage of normal RBCs, sparking debates on the feasibility of the rigid wall assumption. In this work, we perform a computational investigation based on dissipative particle dynamics (DPD) to explore the impact of the deformability of IES on the filtration function of the spleen. We simulate two deformable IES models, namely the passive model and the active model. In the passive model, we implement the worm-like string model to depict the IESs deformation as it interacts with blood plasma and allows RBC to traverse. In contrast, the active model involved regulating the IES deformation based on the local pressure surrounding the slit. To demonstrate the validity of the deformable model, we simulate the filtration of RBCs with varied size and stiffness by IES under three scenarios: 1) a single RBC traversing a single slit; 2) a suspension of RBCs traversing an array of slits, mimicking in vitro spleen-on-a-chip experiments; 3) RBC suspension passing through the 3D spleen filtration unit known as the splenon. Our simulation results of RBC passing through a single slit show that the deformable IES model offers more accurate predictions of the critical cell surface area to volume ratio that dictate the removal of aged RBCs from circulation compared to prior rigid-wall models. Our biophysical models of the spleen-on-a-chip indicates a hierarchy of filtration function stringency: rigid model > passive model > active model, providing a possible explanation of why the spleen-on-a-chip could overestimate the filtration function of IES. We also illustrate that the biophysical model of the splenon enables us to replicate the ex vivo experiments involving spleen filtration of malaria-infected RBCs. Taken together, our simulation findings indicate that the deformable IES model could serve as a mesoscopic representation of spleen filtration function closer to physiological reality, addressing questions beyond the scope of current experimental and computational models and enhancing our understanding of the fundamental flow dynamics and mechanical clearance processes within in the human spleen.

bioengineering↗

bioRxiv2023

A novel, wave-shaped profile of germline selection of pathogenic mtDNA mutations is discovered by bypassing a classical statistical bias.

The shift of the level of disease-causing mtDNA mutations (heteroplasmy) from mother to child is typically negatively correlated with the mothers heteroplasmy (Hm). In other words, mothers with low Hm tend to have children with a higher mutation level (Hch) than their own. In contrast, mothers with high Hm typically see a decrease in heteroplasmy in their children. This trend has been commonly interpreted as a result of a descending germline selection profile, i.e., positive selection at low Hm, gradually turning negative at high Hm. Here we demonstrate, however, that the negative correlation is mostly driven by RTM, or Regression To the Mean, a classical statistical bias. We further show that RTM can be nullified by using the average between the mothers and childs heteroplasmy, as a new variable, instead of the commonly used mothers heteroplasmy in blood. Additionally, we demonstrate that mother/child average is a better approximation of the actual germline heteroplasmy. Moreover, the elimination of RTM revealed a previously hidden wave-shaped HS-profile (positive mother-to-child shift at intermediate average mother-child heteroplasmy, decreasing towards high and low average heteroplasmy). In confirmation of this finding, we show that simulations that involve both wave-shaped HS-profile and RTM, reproduce the observed patterns of inheritance of mtDNA mutations in unprecedented detail. From the health care perspective, the uncovering of the wave-shaped HS-profile (and the removal of the RTM bias) are crucial for families affected by mtDNA disease. From the fundamental perspective, the wave- shaped profile offers a novel understanding of the dynamics of mtDNA in the germline and a novel potential mechanism that prevents the spread of detrimental mtDNA mutations in the population. SignificanceFrom the clinical perspective, the existence of wave-shaped selection may improve predictions and decisions for families affected by mtDNA diseases. From the fundamental perspective, it provides insight into the dynamics of general mtDNA mutations in the germline and in the population, as long as they follow wave-shaped selection profile. In Fig. 1, blue and red arrows represent the direction of expected changes of the heteroplasmy in a lineage with time/generations. With wave- shaped selection (Fig. 1B), a great majority of nascent low- fraction mutations are expected to converge back to zero and vanish. However, due to random intracellular genetic drift, some mutations will, occasionally, expand and enter the range of positive selection. Then they will be expanded by the selection to higher, detrimental levels, and become prone to downstream removal via death of highly mutated germ cells or inability of highly sick individuals to continue their lineage. In this way, the wave-shaped selection may help to prevent the spread of detrimental mutations in the population and in the species. In contrast, if the descending selection profile (Fig. 1A) was in effect, the nascent low heteroplasmy detrimental mutations would have been pushed to intermediate heteroplasmy levels where they will stay longer in hidden disease carriers enabling effective spread of mutation in the population. O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/568140v2_fig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1142cc0org.highwire.dtl.DTLVardef@186002aorg.highwire.dtl.DTLVardef@74d176org.highwire.dtl.DTLVardef@163ca6c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO (Graphic Summary) Pathogenic mtDNA mutations that cause a host of devastating inherited diseases are usually thought to follow an intriguing inheritance trend: Mothers with low levels of mutation (called mother heteroplasmy, Hm) tend to bear children with higher child heteroplasmy (Hch) then their own which constitutes positive Heteroplasmy Shift (HS=Hch-Hm). In contrast, mothers with high heteroplasmy Hm bear children with lower heteroplasmy Hc (negative HS). C_FIG

genomics↗

bioRxiv2023

The 'Stem' and the 'Workers' of the mtDNA population of the cell. Evidence from mutational analysis.

Every cell in our body contains a vibrant population of mitochondria, or, more precisely, of mitochondrial DNA molecules (mtDNAs). Just like members of any population mtDNAs multiply (by replication) and die (i.e., are removed, either by degradation or by distribution into the sister cell in mitosis). An intriguing question is whether all mitochondria in this population are equal, especially whether some are responsible primarily for reproduction and some - for empowering the various jobs of the mitochondrion, oxidative phosphorylation in the first place. Importantly, because mtDNA is highly damaged such a separation of responsibilities could help greatly reduce the conversion of DNA damage into real inheritable mutations. An unexpected twist in the resolution of this problem has been brought about by a recent high-precision analysis of mtDNA mutations (Sanchez-Contreras et al. 2023). They discovered that certain transversion mutations, unlike more common transitions, are not accumulating with age in mice. We argue that this observation requires the existence of a permanent replicating subpopulation/lineage of mtDNA molecules, which are protected from DNA damage, a.k.a. the stem mtDNA. This also implies the existence of its antipode i.e., the worker mtDNA, which empowers OSPHOS, sustains damage and rarely replicates. The analysis of long HiFi reads of mtDNA performed by PacBio closed circular sequencing confirms this assertion.

genomics↗

bioRxiv2022

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals significant contamination with NUMTs, and challenges predominantly purifying selection in late PGCs

The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells (PGCs). Specifically, Floros et al. (Nature Cell Biology 20: 144-51) reported an increase in the synonymity of mtDNA mutations (a sign of purifying selection) between pooled early-stage and late-stage PGCs. We re-analyzed Floros et al. pooled PGC data and noticed that their mutational dataset was significantly contaminated with single nucleotide variants (SNVs) derived from a nuclear sequence of mtDNA origin (NUMT) located on chromosome 5. Contamination was caused by co-amplification of the NUMT sequence by cross-specific PCR primers. Importantly, when we removed NUMT-derived SNVs, the evidence of purifying selection was abolished. In addition to pooled PGCs, Floros et al. reported the analysis of single late-stage PGCs, which were amplified with different sets of PCR primers that cannot amplify the NUMT sequence. Accordingly, we found no NUMT-derived SNVs among single PGCs mutations. Interestingly, single PGC mutations show a decrease of synonymity with increased intracellular mutant fraction. This pattern is incompatible with predominantly negative selection. This suggests that germline selection of mtDNA mutations is a complex phenomenon and that the part of this process that takes place in PGCs may be predominantly positive. However counterintuitive, positive germline selection of detrimental mtDNA mutations has been reported previously and potentially may be evolutionarily advantageous.

genomics↗

bioRxiv2022

The butterfly effect: mutational bias of SARS-CoV-2 affects its pattern of molecular evolution on synonymous and nonsynonymous levels

Evolution is a function of mutagenesis and selection. To analyse the role of mutagenesis on the structure of the SARS-CoV-2 genome, we reconstructed the mutational spectrum, which was highly C>U and G>U biased. This bias forces the SARS-CoV-2 genome to become increasingly U-rich unless selection cancels it. We analysed the consequences of this bias on the composition of the most neutral (four-fold degenerate synonymous substitutions) and the least neutral positions (nonsynonymous substitutions). The neutral nucleotide composition is already highly saturated by U and, according to our model, it is at equilibrium, suggesting that in the future, we dont expect any more increase in U. However, nonsynonymous changes continue slowly evolve towards equilibrium substituting CG-rich amino-acids ("losers") with U-rich ones ("gainers"). This process is universal for all genes of SARS-CoV-2 as well as for other coronaviridae species. In line with the direction mutation pressure hypothesis, we show that viral-specific amino acid content is associated with the viral-specific mutational spectrum due to the accumulation of effectively neutral slightly deleterious variants (losers to gainers) during the molecular evolution. The tuning of a protein space by the mutational process is expected to be typical for species with relaxed purifying selection, suggesting that the purging of slightly-deleterious variants in the SARS-CoV-2 population is not very effective, probably due to the fast expansion of the viral population during the pandemic. Understanding the mutational process can help to design more robust vaccines, based on gainer-rich motifs, close to the mutation-selection equilibrium.

evolutionary biology↗

bioRxiv2022

Prey resources are more important than climatic conditions for predicting the distribution of a broad-ranged apex predator

A current biogeographic paradigm states that climate regulates species distributions at continental scales and that biotic interactions are undetectable at coarse-grain extents. However, recent advances in spatial modelling show that incorporating food resource distributions are important for improving model predictions at large distribution scales. This is particularly relevant to understand the factors limiting distribution of widespread apex predators whose diets are likely to vary across their range. The harpy eagle (Harpia harpyja) is a large raptor, whose diet is largely comprised of arboreal mammals, such as sloths and primates, all with broad distributions across Neotropical lowland forest. Here, we used a hierarchical modelling approach to determine the relative importance of abiotic factors and prey resource distribution on harpy eagle range limits. Our hierarchical approach consisted of the following modelling sequence of explanatory variables: (a) abiotic covariates, (b) prey resource distributions predicted by an equivalent modelling for each prey, (c) the combination of (a) and (b), and (d) as in (c) but with prey resources considered as a single prediction equivalent to prey species richness. Incorporating prey distributions improved model predictions but using solely these biotic covariates still resulted in a high performing model. In the Abiotic model, Climatic Moisture Index (CMI) was the most important predictor, contributing 80 % to model prediction. Three-toed sloth (Bradypus spp.) was the most important prey resource, contributing 57 % in a combined Abiotic-Biotic model, followed by CMI contributing 29 %. Harpy eagle distribution had moderate to high environmental overlap across all prey distributions in geographic space when measured individually, but overlap was substantially lower in environmental space when prey distributions were combined. With strong reliance on prey distributions across its range, harpy eagle conservation programs must therefore consider its most important food resources as a key element in the protection of this threatened raptor.

ecology↗

bioRxiv2022

Habitat resource overlap in two broad-ranged sympatric Neotropical forest eagles

Quantifying resource partitioning between co-occurring species has important ecological and evolutionary implications. Yet, few studies compare resource overlap in both geographic and environmental space. We test whether the habitat requirements of two closely related Neotropical forest eagles, the crested eagle (Morphnus guianensis) and harpy eagle (Harpia harpyja), differ at fine and coarse resolutions across their shared geographic range. Using landcover and topographic covariates, we quantified resource overlap first using higher resolution (30 arc-sec data) generalized linear models (GLMs), and second using coarser-grain (2.5 arc-min data) environmental ordination. The distribution of both eagles was largely explained by canopy species richness and structural complexity with evergreen forest, but with differing responses to landcover and topography, particularly with the harpy eagle more likely in areas of dense evergreen forest. Both eagles were negatively associated with mosaic forest, with this relationship stronger for the crested eagle. Harpy eagle distribution was restricted by higher elevation and terrain roughness, compared to the crested eagle, whose distribution was more restricted by canopy species richness and structure. From the GLMs, resource overlap was > 92 % in geographical space but reduced to 64 % in environmental space. From ordination, resource overlap was 76 % in environmental space, with randomization tests supporting equivalent environmental space for both eagles. Our results suggest that at the biogeographical scale, crested and harpy eagles share environmental space, but there may be subtle differences in fine-scale habitat preference. We recommend habitat resource overlap be assessed in both geographical and environmental space at multiple resolutions to capture the inherent variability in environmental conditions available to co-occurring species.

ecology↗