Biology subjects

Barteri, F.

Publications and source records attributed to Barteri, F..

7 recordsLinked to original sources

bioRxiv2026

Convergent Amino-Acid Substitutions Link Primate Longevity to Male-Fertility Genes

Maximum lifespan varies widely among mammals, but the genomic basis of this variation remains incompletely understood. We used body-mass-corrected longevity and a phylogenetically informed phenotype-shift framework to compare 126 primate species, selecting seven long-lived and six short-lived species for convergent amino-acid substitution analysis. Stringent pooling across species identified 1,068 recurrent phenotype-associated positions in 934 genes. These genes showed significant agreement with mammal-wide longevity candidates, with 226 genes shared compared with 120 expected by chance (1.88-fold enrichment; P = 1.16 x 10exp-22). Functional analysis detected 17 significant terms, with the strongest coherent signal involving male infertility and decreased male fertility. Our results show that focused primate sampling recovers a non-random component of the broader mammalian longevity signal and point to male reproductive biology as a promising direction for investigating the evolution of lifespan.

evolutionary biology↗

bioRxiv2026

Phenotype shift scores reveal the scale and phylogenetic structure of phenotypic differentiation in primates.

Continuous traits evolve unevenly across phylogenies, producing patterns of phenotypic differentiation shaped by both shared ancestry and lineage-specific change. Identifying exceptionally differentiated species pairs may therefore improve genome-phenome comparisons, but existing approaches rarely rank such contrasts across entire trees. Here we introduce the Phenotype Shift Score (PSS), a phylogenetic comparative framework integrating model-based trait divergence, observed trait range and patristic distance. Applying PSS to 153 continuous primate traits reveals trait-specific distributions of extreme differentiation across evolutionary depth. Body and brain mass show deeper-than-expected extremes under fitted Brownian motion or Ornstein-Uhlenbeck nulls, whereas body-size-adjusted brain mass localizes recent differentiation within cercopithecid lineages, complementing published branchwise reconstructions. PSS-informed groups produce more selective and more strongly enriched comparative-genomic signals than groups based on absolute phenotypic extremes. PSS is implemented in the open-source R package phyloPSS, with pairwise results available through the Primate Genome-Phenome Archive.

evolutionary biology↗

bioRxiv2025

A phylogenetic protein-coding genome-phenome map of complex traits across 224 primate species.

Complex traits arise from networks of coding and regulatory loci, making it difficult to resolve their genetic basis. Macroevolutionary studies leverage tens of millions of years of divergence across species to uncover fixed genomic changes invisible to within-species approaches, such as GWAS, offering a complementary framework for generating hypotheses in biomedical research. Here, we present the first phylogenetic protein-coding primate-wide genome-phenome map (P3GMap), spanning 200 curated traits across 224 primate species, which we release through the Primate Genome-Phenome Archive (PGA, https://pgarchive.github.io). Using two complementary approaches, convergent amino acid substitutions and relative evolutionary rates, we linked protein-coding variation to complex phenotypes and identified thousands of candidate gene-trait associations, including lineage-specific signals related to diet, immunity, and lifespan. One sentence summaryCross-species genome-phenome mapping in primates reveals thousands of protein-coding variants linked to the evolution of complex traits.

evolutionary biology↗

bioRxiv2022

CAAStools, a toolbox to identify and test Convergent Amino Acid Substitutions.

BackgroundCoincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for pre-defined groups of species representing the phenotypic values targeted by the user. Implementation and availabilityCAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples. Supplementary informationSupplementary data are available.

bioinformatics↗

bioRxiv2021

Comparative analysis of mammal genomes unveils key genomic variability for human lifespan.

Mammals vary 100-fold in their maximum lifespan. This enormous variation is the result of the adaptations of each species to their own biological trade-offs and ecological conditions. Comparative genomics studies have demonstrated that the genomic factors underlying the lifespans of species and the longevity of individuals are shared across the tree of life. Here, we set out to compare protein-coding regions across the mammalian phylogeny, aiming to detect individual amino acid changes shared by the most long-lived mammal species and genes whose rates of protein evolution correlate with longevity. We discovered a total of 2,737 amino acid changes in 2,004 genes that distinguish long- and short-lived mammals, significantly more than expected by chance (p=0.003). The detected genes belong to pathways involved in regulating lifespan, such as inflammatory response and hemostasis. Among them, a total 1,157 amino acids, located in 996 different genes, showed a significant association with maximum lifespan in a phylogenetically controlled test. Interestingly, most of the detected amino acids positions do not vary in extant human populations (>81.2%) or have allele frequencies below 1% (99.78%), Consequently, almost none could have been detected by Genome-Wide Association Studies (GWAS). Additionally, we identified four more genes whose rate of protein evolution correlated with longevity in mammals. Crucially, SNPs located in the detected genes explain a larger fraction of human lifespan heritability than expected by chance, successfully demonstrating for the first time that comparative genomics can be used to enhance the interpretation of human GWAS. Finally, we show that the human longevity-associated proteins coded by the detected genes are significantly more stable than the orthologous proteins from short-lived mammals, strongly suggesting that general protein stability is linked to increased lifespan.

genomics↗

bioRxiv2020

Evolutionary phenome-genome analysis of cranial suture closure in mammals

Cranial sutures are growth and stress diffusion sites that connect the bones protecting the brain. The closure of cranial suture is a key feature of mammalian late development and evolution, which can also lead to head malformations when it occurs prematurely (craniosynostosis). To unveil the phenotypic and genetic causes of suture closure in evolution, we examined 48 mammalian species searching for (i) causal links between suture patency, brain size, and diet using phylogenetic path analysis; and (ii) instances of genome-phenome convergence amino acid substitutions. Here we show that brain size and the anteroposterior order of ossification of the skull are the two main causes of sutures patency in evolution. We also identified three novel candidate genes for suture closure in evolution (HRNR, KIAA1549, and TTN), which have never been reported in clinical studies of craniosynostosis. Our results suggest that different genetic pathways underlie cranial suture closure in evolution and disease.

evolutionary biology↗

bioRxiv2019

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.

genomics↗