Biology subjects

Venditti, C.

Publications and source records attributed to Venditti, C..

16 recordsLinked to original sources

bioRxiv2026

Indirect genomic effects shape cancer risk across species

Tumour prevalence varies dramatically throughout the animal kingdom despite broadly conserved cellular and developmental processes, raising the question of how evolution has shaped susceptibility 1,2. Here, we link macroevolutionary variation in tumour prevalence to gene-level selection by integrating comparative genomics data from 109 species of birds and mammals using a Bayesian phylogenetic framework to estimate pangenome-wide rates of genetic evolution across >150 million years of evolutionary change. We identify 3,206 genes in which natural selection is associated with shifts in tumour prevalence, with more than 80% of which are linked to reduced prevalence, suggesting pervasive selection for cancer suppression. Using causal phylogenetic inference, we show that genes associated with reduced tumour prevalence act predominantly through indirect effects on body size, revealing growth as a key mediator of cancer risk across species. In contrast, genes associated with increased tumour prevalence exert direct effects independent of body size. Finally, at the species-level, we demonstrate that exceptionally low rates of benign tumours do not necessarily coincide with reduced malignancy, revealing that benign and malignant tumour processes are evolutionarily decoupled. Together, these results reveal how natural selection has fine-tuned the link between genotype, phenotype, and cancer risk across species.

evolutionary biology↗

bioRxiv2025

A functional Red List Index for monitoring trends in functional diversity

Functional diversity supports ecosystem function and resilience but is in decline due to ongoing extinctions. Despite this, no functional diversity metrics are included in the set of indicators adopted by governments to measure progress towards the Global Biodiversity Framework. Monitoring changes in functional diversity is essential to understand differences between taxonomic and functional diversity trends. The Red List Index (RLI) is a widely used metric in conservation policy, and tracks trends in aggregate extinction risk across sets of species over time. We present a functional Red List Index (fRLI), which weights species by their morphological uniqueness at either local or global scales, to indicate the risk that future extinctions could pose to functional diversity. We applied the fRLI on birds and found higher aggregate extinction risk for both local and global fRLI compared with the standard RLI. Species with higher local uniqueness were more likely to be at higher risk of extinction while we found no difference for globally unique species. Globally or locally unique species were not more likely to show escalation in extinction risk between 1988 and 2024 than less unique species; however, locally unique birds had a lower proportion of their resident range covered by site-based conservation measures, leaving them vulnerable to future decline. The fRLI provides a tool to monitor the impact of extinction risk on functional diversity and could be applied to other taxonomic groups with comprehensive or representative coverage of Red List assessments and trait data.

ecology↗

bioRxiv2025

CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family

Integrated datasets linking traits, spatial distributions, environmental variables and phylogenies are essential for comparative research, but remain limited for many plant taxa, including those which are most threatened. Cactaceae are a morphologically and ecologically diverse succulent family that are iconic components of ecosystems across the Americas, and face high extinction risk. To support future comparative research, we present CactEcoDB (The Cactus Ecological Database), an Open Access dataset of curated spatial, ecological, trait, phylogenetic, and diversification data for over 1,000 cactus species. CactEcoDB includes species-level trait data, geographic occurrence records, environmental variables, range size estimates, speciation rates, and the largest time-calibrated phylogeny of cacti to date. By integrating these diverse data in a single platform, CactEcoDB enables analyses of trait evolution, trait-environment interactions, biogeography, climatic niche evolution, and macroevolutionary dynamics in one of the most celebrated and threatened plant families.

evolutionary biology↗

bioRxiv2025

Phylogenetic meta-analysis implicates large brains and our unusual posture in human handedness

Humans exhibit a striking and near-universal population-level right-hand preference, an evolutionary singularity unmatched among primates. Despite its pervasiveness, the origins of this lateralisation remain poorly understood. Here, we combine phylogenetic comparative methods with meta-analysis to investigate manual lateralisation across 41 anthropoid species (n = 2,025), testing longstanding eco-evolutionary hypotheses for handedness direction (MHI) and strength (MABSHI). Our models reveal significant phylogenetic signal for both traits and identify Homo sapiens as an evolutionary outlier, exhibiting exceptional rightward bias and strength relative to phylogenetic expectations. However, this outlier status disappears when brain size (endocranial volume, ECV) and intermembral index (IMI) are included, suggesting these factors are central to the emergence of human handedness. We also show that high MABSHI evolved early in hominin evolution, while MHI increased to unparalleled levels with the appearance of the genus Homo. Our findings implicate bipedalism and neuroanatomical expansion as key drivers of uniquely human lateralisation, while also revealing broader ecological patterns shaping handedness across primates. This work provides a framework for disentangling human-specific adaptations from general primate trends in the evolution of behavioural asymmetries.

evolutionary biology↗

bioRxiv2025

Threat reduction must be coupled with targeted recovery programmes to conserve global bird diversity

Biodiversity is undergoing severe declines while threats to natural populations continue to escalate worldwide. Ambitious international commitments have been made to preserve biodiversity, with the goal of preventing extinctions and maintaining ecosystem resilience, yet the efficacy of large-scale protection remains unclear. Here we use a trait-based approach to show that global actions - such as the immediate abatement of all threats across at least half of species ranges for [~]10,000 bird species - will only prevent half of projected species extinctions and functional diversity loss attributable to current and future threats in the next 100 years. Nonetheless, targeted recovery programmes prioritizing protection of the 100 most functionally unique threatened birds could avoid 68% of projected functional diversity loss. Actions targeting habitat loss and degradation will prevent the greatest number of species extinctions and proportion of functional diversity loss relative to other drivers of extinction, whereas control of hunting and collection and disturbance and accidental mortality would save fewer species but disproportionately boost functional richness. These findings show that conservation of avian diversity requires action partitioned across all drivers of decline, and highlights the importance of understanding and mitigating the ecological impacts of species extinctions predicted to occur even under optimistic levels of conservation action.

ecology↗

bioRxiv2024

The coevolution of encephalization and manual dexterity in hominins and other primates

The human hand is one of our most remarkable features. We have long, opposable thumbs and a suite of other features argued to be adaptations for interacting with and manipulating our environment, literally extending the reach of our cognitive powers. Consequently, enhanced manipulative dexterity, tool use and increased brain size are considered key features of how our ancestors evolved. This hypothesis predicts that anatomical dexterity and brain size co-evolved, and that this should be evident in the morphology of the hand. To test this hypothesis and to understand how hominin evolution may have deviated from any general primate trend, we collected a dataset of finger length, thumb length, and brain size across 94 extinct and extant species of primates. Using phylogenetic comparative methods, we reveal a strong primate-wide association between brain size and relative thumb length. We further demonstrate that this general association accurately predicts the co-evolution of these traits in hominins. Whilst hominins have significantly long thumbs compared to other primates, we infer that they have arisen from the same underlying evolutionary process acting across the whole primate order: increasing manipulative ability associated with specialized neural control processes. The relationships we recover are consistent with positive feedback between manipulation, tool use and cognition and therefore may go some way towards explaining evolutionary trends towards larger brain sizes among primates, and particularly in hominins. Our results emphasize the role of manipulative abilities in cognitive evolution and emphasize how neural and bodily adaptations are interconnected.

evolutionary biology↗

bioRxiv2024

Climatic-environmental influences on hominin brain size over the last 5 million years

A large brain relative to body mass is considered a distinguishing hominin trait. It has frequently been related to a suite of social, behavioral, technological, and other cognitive adaptations that differentiate humans from other species. The processes underlying large brain size evolution have therefore been a subject of rigorous scientific debate. Many hypotheses have been proposed to explain how climate and environment drive the selection of larger brain sizes, but monotonic influences of climate-environmental selective pressures are often assumed and rarely have between- and within-species effects been considered. Here, we apply Bayesian phylogenetic comparative techniques to the hominin fossil record to test the effect of climatic and environmental pressures (C-E) on brain size evolution, whilst simultaneously accounting for body mass and chronological age. We find that colder and more variable temperatures have a positive within-species effect on brain size evolution, likely related to biological adaptations to mitigate against hypothermia. However, in Homo, the strength of this effect diminishes over time suggesting that in later species (Homo sapiens and Homo neanderthalensis) brain sizes were less affected by C-E conditions.

evolutionary biology↗

bioRxiv2024

Punctuational evolution is pervasive in distal site metastatic colonization

The evolution of metastasis represents a lethal stage of cancer progression. Yet, the evolutionary kinetics of metastatic disease remain unresolved. Here, using single cell CRISPR-Cas9 lineage tracing data, we show that in metastatic disease, gradual molecular evolution is punctuated by episodes of rapid evolutionary change associated with lineage divergence. By measuring punctuational effects across the metastatic cascade, we show that punctuational effects contribute more to the molecular diversity at distal site metastases compared to the paired primary tumor, suggesting qualitatively different modes of evolution may drive primary and metastatic tumor progression. This is the first empirical evidence for distinct patterns of molecular evolution at early and late stages of metastasis and demonstrates the complex interplay of cell intrinsic and extrinsic factors that shape lethal cancer.

cancer biology↗

bioRxiv2024

Hominin brain size increase has emerged from within-species encephalization

The fact that rapid brain size increase was clearly a key aspect of human evolution has prompted many studies focussing on this phenomenon1-4, and many suggestions as to the underlying evolutionary patterns and processes5-10. No study to date has however separated out the contributions of change through time within-vs. between-hominin species whilst simultaneously incorporating effects of body size. Using a phylogenetic approach never applied before to palaeoanthropological data, we show that brain size increase across ~ 7 million years of hominin evolution arose from increases within individual species which account for an observed overall increase in relative brain size. Variation among species in brain size after accounting for this effect is associated with body mass differences but not time. In addition, our analysis also reveals that the within-species trend escalated in more recent lineages, implying an overall pattern of accelerating brain size increase through time.

paleontology↗

bioRxiv2023

Co-evolutionary dynamics of mammalian brain and body size

Despite decades of comparative studies, fundamental questions remain about how brain and body size co-evolved. Divergent explanations exist concurrently in the literature for phenomena such as variation in brain relative to body size, variability in the scaling relationship across taxonomic levels and between taxonomic groups, and purported evolutionary trends. Here we resolve these issues using a comprehensive dataset of brain and body masses across the mammal radiation, and a method enabling us to study brain relative to body mass evolution while estimating their evolutionary rates along the branches of a phylogeny. Contrary to the rarely questioned assumption of a log-linear relationship, we find that a curvilinear model best describes the evolutionary relationship between log brain mass and log body mass. This model greatly simplifies our understanding of mammalian brain-body co-evolution: it can simultaneously explain both the much-discussed taxon-level effect and variation in slopes and intercepts previously attributed to complex scaling patterns. We also document substantial variation in rates of relative brain mass evolution, with bursts of change scattered through the tree. General trends for increasing relative brain size over time are found in only three mammalian orders, with the most extreme case being primates, setting the stage for the uniquely rapid directional increase that ultimately produced the computational powers of the human brain.

evolutionary biology↗

bioRxiv2022

Trait diversity metrics can perform well with highly incomplete datasets

O_LICharacterizing changes in trait diversity at large spatial scales provides insight into the impact of human activity on ecosystem structure and function. However, the approach is often based on trait datasets that are incomplete and unrepresentative, with uncertain impacts on trait diversity estimates. C_LIO_LITo address this knowledge gap, we simulated random and biased removal of data from a near complete avian trait dataset (9579 species) and assessed whether trait diversity metrics were robust to data incompleteness with and without using imputation to fill data gaps. Specifically, we compared two commonly used metrics each calculated with two methods: trait richness (calculated with convex hulls and trait probabilities densities) and trait divergence (calculated with distance-based Rao and trait probability densities). C_LIO_LIWithout imputation, estimates of global avian trait diversity (richness and divergence) were robust when 30-70% of species had missing data for four out of 11 continuous traits, depending on severity of bias and the method used. However, when missing traits were imputed based on present morphological trait data and phylogeny, trait diversity metrics consistently remained representative of the true value, even when 70% of species were missing data for four out of 11 traits and data were not missing at random (biased with respect to body mass). Trait probability densities and distance-based Rao were particularly robust to missingness and bias when combined with imputation, with convex hull-based trait richness being less reliable. C_LIO_LIExpanding global morphometric datasets to represent more taxa and traits, and to quantify intraspecific variation, remains a priority. In the meantime, our results show that widely used methods can successfully quantify large-scale trait diversity even when data are missing for two-thirds of species, so long as missing traits are estimated using imputation. C_LI

ecology↗

bioRxiv2020

Shrinking of fish under warmer temperatures decrease dispersal abilities and speciation rates

There is an ongoing debate as to whether fish body size will decrease with global warming and how body size changes may impact dispersal abilities and speciation rates. Although theory predicts that, when fish face warmer temperatures, they grow to smaller adult sizes, see a reduction in their ability to move, and increase their probability of speciation, evaluations of such predictions are hampered owing to the lack of empirical data spanning both wide temporal and geographical scales. Here, using phylogenetic methods, temperature, and 21,895 occurrences for 158 worldwide-distributed species of fish, we show that smaller fish have occurred in warmer waters for over 150 million years and across marine and freshwater realms. Smaller fish have historically moved the shortest distances and at low speeds. In addition, small fish display the lowest probability of giving rise to new species. Further, we found that species of fish that displayed high speeds of geographical movement and rates of size evolution experienced higher rates of temperature change in their lineage. Taking these results together, global warming predicts a future where smaller fish that have reduced ability to move over aquatic systems will be more prevalent, in turn, this will result in fewer species contributing global biodiversity.

evolutionary biology↗

bioRxiv2020

Phenotypic reconstruction of the last universal common ancestor reveals a complex cell

A fundamental concept in evolutionary theory is the last universal common ancestor (LUCA) from which all living organisms originated. While hypotheses regarding the phenotype of LUCA do exist, most are at best based on gene presence or absence. However, despite recent attempts to link genes and phenotypic traits in prokaryotes, it is still inherently difficult to predict phenotype based on the presence or absence of genes alone. Here, we apply a novel approach based on phylogenetically informed ancestral character reconstruction with 22 fundamental descriptors of prokaryotic cells to reconstruct LUCAs phenotype. We infer that the last universal common ancestor of all living organisms was likely an ovoid cell with a large genome, which probably had a cell wall and was actively motile. Potentially obtaining energy from the oxidation of inorganic compounds, tolerant of saltwater and thriving at temperatures above 70{degrees}C, LUCA was probably found living freely in anaerobic conditions in water of neutral pH. Our results depict LUCA as likely to be a far more complex cell than has previously been proposed, challenging the evolutionary model of increased complexity through time in prokaryotes. Given current estimates for the emergence of LUCA we suggest that early life very rapidly evolved considerable cellular complexity.

evolutionary biology↗

bioRxiv2018

Epidemiologal investigation of an Acinetobacter baumannii outbreak using Core Genome Multilocus Sequence Typing

Carbapenem-resistant (CR) Acinetobacter baumannii is a serious nosocomial pathogen able to cause a variety of serious, often life-threatening infections and outbreaks. We aimed to investigate the molecular epidemiology of clinical isolates of CR-A. baumannii from an outbreak occurred in the intensive care unit (ICU) of our hospital.\n\nFrom January to April 2017, 13 CR-A. baumannii isolates were collected at the \"L. Spallanzani\" hospital, Rome, Italy; typing was performed by repetitive extragenetic palindromic-based (rep)- PCR-based DiversiLab system and WGS data were used for in silico analysis of traditional MLST types, for identifying resistance genes and for core genome multi locus sequence typing (cgMLST) analysis. Epidemiological data were obtained from hospital records.\n\nStrains were cultured from 7 patients treated in the ICU of our hospital; all isolates showed a multi-drug resistant (MDR) profile, carrying the blaOXA-23 carbapenemase. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group while the cgMLST approach, which uses 2690 gene targets to characterize the gene-by-gene allelic profile of A. baumannii, highlighted the presence of two cluster types. These results allowed us to identify two patients who entered the ICU already colonized by two different strains of CR-A. baumannii; we hypothesize that these two patients could be the source of two separate transmission chains.\n\nOur results show that whole-genome-DNA sequencing by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.

molecular biology↗

bioRxiv2018

Extreme and rapid bursts of functional adaptations shape bite force in amniotes

Adaptation is the fundamental driver of functional and biomechanical evolution and can be linked to rates of phenotypic trait evolution. Significant shifts in evolutionary rates are seen as instances of exceptional adaptation. However, whether or not signatures of exceptional adaptations (elevated rates) can be distinguished from general adaptations (background rate) in biomechanical traits remains to be tested in a robust statistical framework. Here, we apply a recently developed phylogenetic statistical approach for detecting exceptional adaptations in bite force, in a large group of terrestrial vertebrates, the amniotes. Our results show that bite force in amniotes evolved through multiple bursts of exceptional changes, whereby whole groups - including Darwin';s finches, maniraptoran dinosaurs (group of non-avian dinosaurs including birds), anthropoids and hominins (the group of species including modern humans) - experienced significant rate increases compared to the background rate. However, in most parts of the amniote tree of life we find no exceptional rate increases, indicating that coevolution with body size was primarily responsible for the patterns observed in bite force. Our approach represents a template for future studies in functional morphology and biomechanics, where exceptional functional adaptations can be quantified and potentially linked to specific ecological factors underpinning major evolutionary radiations.

evolutionary biology↗

bioRxiv2017

150 million years of sustained increase in pterosaur flight efficiency

The long-term accumulation of biodiversity has been punctuated by remarkable evolutionary transitions that allowed organisms to exploit new ecological opportunities, and often resulted in large radiations of species. The Mesozoic flying reptiles - pterosaurs - which dominated the skies for over 150 million years (Myr), were the product of such a transition. The ancestors of pterosaurs were small and likely bipedal early archosaurs, which were certainly well adapted to terrestrial locomotion. More than 220 Myr ago, at some point in the Triassic, pterosaurs took flight and subsequently appear to have become capable and efficient flyers. However, the evolutionary processes that led to this efficiency remain enigmatic. Given the lack of proto-pterosaurs it is difficult to study how flight first evolved in this group, but we can test hypotheses about evolutionary changes to the energetics of locomotion following the transition to flight. Early pterosaurs were challenged by the c ...

evolutionary biology↗