Biology subjects

Aristide, L.

Publications and source records attributed to Aristide, L..

6 recordsLinked to original sources

bioRxiv2026

Lineage-specific histories rather than shared drivers shape olfactory evolution in New World monkeys

Variation in primate olfactory receptor gene repertoires has been linked to shared ecological and sensory drivers, including diet, diurnality, and colour vision. Yet within anthropoids, each link rests on a single lineage, leaving unclear whether this variation reflects a shared response to these drivers or lineage-specific histories. Here, we combine genomic data from 80 New World monkey species with CT-based olfactory anatomy and ecological data to investigate the evolutionary processes underlying repertoire variation. Ecological and sensory variables explain little of this variation; even routinely trichromatic, leaf-eating howler monkeys have repertoires of unremarkable size. Instead, convergent reductions in repertoire size arose through distinct genomic routes: extensive gene inactivation in titi monkeys and large structural deletions in squirrel monkeys. Owl monkeys, the only anthropoids that reverted to nocturnality, retained rather than expanded a large ancestral repertoire shared with diurnal capuchins, and instead enlarged their olfactory bulb. Repertoire size covaries with olfactory bulb volume across the radiation, but only partially within lineages: squirrel monkeys show the converse, losing receptors without a matching bulb reduction. Thus, olfactory evolution in New World monkeys reflects historical contingency rather than a shared response, with convergent changes in repertoire size and partial decoupling of genomic and anatomical evolution.

evolutionary biology↗

bioRxiv2025

Parallel genomic remodeling associated with independent terrestrialization events in arthropods

The repeated transition from aquatic to terrestrial environments (terrestrialization) has shaped the evolutionary trajectory of many animal lineages, yet the genomic basis of this ecological shift remains incompletely understood. Arthropods, with multiple independent terrestrialization events, provide a powerful system to investigate whether parallel genomic changes underlie adaptation to land. Here, we present a phylum-wide comparative phylogenomic analysis of 309 arthropod species representing aquatic and terrestrial lineages, using gene family evolutionary dynamics and directional selection analyses to uncover shared genomic strategies associated with life on land. We identified thousands of orthogroups showing parallel expansions or contractions across the three main lineages that colonized land (Arachnida, Myriapoda, and Hexapoda), of which a significant proportion also exhibited lineage-specific shifts in selective pressure. Functional enrichment of these orthogroups revealed functional convergence on processes such as oxidative stress response, transmembrane transport, energy metabolism, exoskeleton formation, and moulting regulation. Notably, parallel evolution in aquaporins, solute carriers, cytochrome P450s, superoxide dismutases, and heat shock proteins suggests that a conserved terrestrialization toolkit underlies independent colonization events. Additionally, parallel remodeling of key developmental and immune signaling pathways highlights the role of regulatory and structural innovations in adapting to terrestrial challenges. Our results provide the first large-scale genomic evidence of parallel molecular evolution driving arthropod terrestrialization and emphasize the power of comparative genomics to reveal shared solutions to ecological transitions across deep evolutionary timescales.

evolutionary biology↗

bioRxiv2025

Principles of neocortical organisation and behaviour in primates

One sentence summaryThe study of brain MRI from 70 different primate species reveals a fundamental principle of neocortical organisation and behaviour driven by mechanical morphogenesis. The development and evolution of neocortical organisation is typically explained by the interaction of two fundamental factors: genetics and experience-dependent processes. Morphogens and signalling molecules would orchestrate the formation of neocortical areas and connection networks, which are later refined through exposure to environmental stimuli. Evolutionary changes to these genetic programs are thought to account for the diversity of brains and behaviours observed in extant species. However, our phylogenetic comparative study of primate neuroanatomy and behaviour shows this view is incomplete. Using brain MRI from 70 primate species we observed that not only the degree of folding but also the folding pattern changes continuously with brain volume, independently of phylogenetic position. To better understand the consequences of this continuity we focused on New and Old World monkeys which diverged approximately 47 million years ago. Large New World monkeys, such as capuchins, have a significantly larger and more folded neocortex than many of their close phylogenetic relatives, whose brains are barely folded. Notably, in addition to folding, their thickness and connectivity patterns were almost identical to those of phylogenetically distant Old World monkeys. Combined analyses of MRI and endocasts from 105 primate species indicated that the highly folded neocortex of large New World monkeys evolved independently from a common ancestor with a small, unfolded brain. Remarkably, across all 70 species, behavioural similarity correlated substantially more with neuroanatomical similarity than with phylogenetic similarity. Our results challenge the prevailing explanation of the development and evolution of neocortical organisation. We propose that the "capuchin anomaly" can be resolved by incorporating mechanical morphogenesis, alongside genetics and experience, as a third fundamental factor. Growth-driven mechanical instabilities would produce similar neuroanatomical organisation patterns and behaviours, emerging independently of the specific genetic determinants of that growth.

neuroscience↗

bioRxiv2022

Parallel duplication and loss of aquaporin-coding genes during the 'out of the sea' transition paved the way for animal terrestrialization

One of the most important physiological challenges animals had to overcome during terrestrialization (i.e., the transition from sea to land) is water loss, which alters their osmotic and hydric homeostasis. Aquaporins are a superfamily of membrane water transporters heavily involved in osmoregulatory processes. Their diversity and evolutionary dynamics in most animal lineages remain unknown, hampering our understanding of their role in marine-terrestrial transitions. Here, we interrogated aquaporin gene repertoire evolution across the main terrestrial animal lineages. We annotated aquaporin-coding genes in genomic data from 458 species from 7 animal phyla where terrestrialization episodes occurred. We then explored aquaporin gene evolutionary dynamics to assess differences between terrestrial and aquatic species through phylogenomics and phylogenetic comparative methods. Our results revealed parallel aquaporin-coding gene duplications in aquaporins during the transition from marine to non-marine environments (e.g., brackish, freshwater and terrestrial), rather than from aquatic to terrestrial ones, with some notable duplications in ancient lineages. Contrarily, we also recovered a significantly lower number of superaquaporin genes in terrestrial arthropods, suggesting that more efficient oxygen homeostasis in land arthropods might be linked to a reduction in this type of aquaporins. Our results thus indicate that aquaporin-coding gene duplication and loss might have been one of the key steps towards the evolution of osmoregulation across animals, facilitating the out of the sea transition and ultimately the colonisation of land.

evolutionary biology↗

bioRxiv2022

MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies

AO_SCPLOWBSTRACTC_SCPLOWWith the advent of high throughput sequencing, the amount of genomic data available for animals (Metazoa) species has bloomed over the last decade, especially from transcriptomes due to lower sequencing costs and easier assembling process compared to genomes. Transcriptomic data sets have proven useful for phylogenomic studies, such as inference of phylogenetic interrelationships (e.g., species tree reconstruction) and comparative genomics analyses (e.g., gene repertoire evolutionary dynamics). However, these data sets are often analyzed following different analytical pipelines, particularly including different software versions, leading to potential methodological biases when analyzed jointly in a comparative framework. Moreover, these analyses are computationally expensive and not affordable for a large part of the scientific community. More importantly, assembled transcriptomes are usually not deposited in public databases. Furthermore, the quality of these data sets is hardly ever taken into consideration, potentially impacting subsequent analyses such as orthology and phylogenetic or gene repertoire evolution inference. To alleviate these issues, we present Metazoan Assemblies from Transcriptomic Ensembles (MATEdb), a curated database of 335 high-quality transcriptome assemblies from different animal phyla analyzed following the same pipeline. The repository is composed, for each species, of (1) a de novo transcriptome assembly, (2) its candidate coding regions within transcripts (both at the level of nucleotide and amino acid sequences), (3) the coding regions filtered using their contamination profile (i.e., only metazoan content), (4) the longest isoform of the amino acid candidate coding regions, (5) the gene content completeness score as assessed against the BUSCO database, and (6) an orthology-based gene annotation. We complement the repository with gene annotations from high-quality genomes, which are often not straightforward to obtain from individual sequencing projects, totalling 423 high-quality genomic and transcriptomic data sets. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, that will be analyzed following the same pipeline and be permanently stored in public repositories. We believe that MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open and collaborative science.

evolutionary biology↗

bioRxiv2019

Characterizing and comparing phylogenetic trait data from their normalized Laplacian spectrum

The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no non-parametric comprehensive framework for characterising and comparing patterns of phenotypic evolution. Here we build on a recently introduced approach for using the phylogenetic spectral density profile to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for non-parametric analysis of phylogenetic trait data. We show how to construct the spectral density profile of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the spectral density profile to successfully cluster phylogenetic trait data into meaningful groups and to characterise the phenotypic patterning within those groups. We furthermore demonstrate how the spectral density profile is a powerful tool for visualising phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical datasets: a comprehensive dataset of traits involved in song, plumage and resource-use in tanagers, and a high-dimensional dataset of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework.

evolutionary biology↗