Biology subjects

Vinicius, L.

Publications and source records attributed to Vinicius, L..

9 recordsLinked to original sources

bioRxiv2026

geoGraph: Connectivity modelling across geographic space with hexagonal discrete global grids

1. Estimating the movement and connectivity of organisms across landscapes is central to research in ecology and evolutionary biology. Although graph-based approaches representing geographic space as weighted networks provide a flexible and computationally efficient framework for such analyses, existing tools either perform their computations only on rectangular raster grids, thus introducing systematic directional and area distortions at global scales, or rely on bespoke pipelines that limit the general applicability of recent hexagonal-grid analyses. 2. To overcome these shortcomings, here we present geoGraph, an R package that brings graph-based spatial modelling to discrete global hexagonal grids. By representing landscapes on an equal-area hexagonal tessellation of the sphere, geoGraph enables global-scale analysis without projection distortion while retaining the flexibility of the graph framework and the performance of the graph and RBGL/Boost libraries. The package integrates both raster- and vector-based GIS data into a single cost surface, supports custom grids at various resolutions, and provides a complete pipeline from raw GIS layers to graph-algorithmic outputs, together with tools for visualising and interactively editing graphs. 3. We illustrate geoGraph by revisiting previous studies of isolation by distance among human populations in the Human Genome Diversity Project panel. At a global scale, restricting movement to land raised the correlation between geographic and genetic distance from r = 0.74 (great-circle) to r = 0.84. On a finer grid within Asia, accounting for terrain ruggedness improved the fit, with the best-fitting models implying reduced movement across the Himalaya and Tibetan Plateau. These analyses demonstrate that geoGraph can model movement and connectivity appropriate to the desired spatial scale and that the level of geographic realism required is itself scale-dependent. 4. By combining discrete global grids with the power of graph algorithms, geoGraph enables seamless connectivity analysis from landscape to global scales. It is broadly applicable across landscape genetics, phylogeography, conservation planning, and studies of human dispersal, and is particularly suited to large-scale problems that rectangular-raster tools cannot address without distortion.

bioinformatics↗

bioRxiv2026

Cultural norms of exogamy and mobility shape hunter-gatherer genetic evolution

Through a hunting and gathering lifestyle, humans have managed to thrive across all terrestrial ecosystems. A key adaptive feature enabling this ecological success is the ability of hunter-gatherer societies to maintain high levels of genetic diversity despite ecological and demographic shocks, but the mechanisms underlying this resilience are poorly understood. Here we integrate genomic, demographic, mobility and ethnographic data from two Central African hunter-gatherer populations to show that genetic diversity emerges from interacting effects of population size, mobility and cultural norms governing marriage. We first demonstrate direct selection against background homozygosity: even modest increases in runs of homozygosity, in the near absence of close-kin marriage, are associated with reduced reproductive success. Despite regional differences in effective population size, clustering of relatives, sedentism and exogamy rules, overall levels of homozygosity are similarly low in both populations. These shared genetic outcomes are achieved through distinct strategies: in one region, strict exogamy combined with high lifetime mobility limits local relatedness, whereas in the other, more relaxed exogamy norms are offset by increased male mate-search distances that reduce offspring homozygosity. Together, our results show that human populations flexibly adjust mobility and social norms to demographic constraints to preserve genetic diversity and avoid fitness costs, revealing culture as a central component of human adaptation.

genetics↗

bioRxiv2025

Pan-African metapopulation model explains Homo sapiens genetic and morphological evolution

A growing body of evidence has challenged the traditional assumption of a single-region origin for Homo sapiens, suggesting instead that our species originated from multiple geographically distinct populations in Africa, which intermittently exchanged genes and culture. However, our understanding of how this Pan-African metapopulation would have evolved through time is still limited. Furthermore, the drivers of such changes are uncertain, and quantitative models of the respective contributions of different African regions are lacking. Here we provide a complete reconstruction of the meta-population dynamics over the last 200,000 years by quantitatively integrating an ecological niche model, informed by archaeological sites, within a spatially explicit population genetic framework. The inferred metapopulation dynamics account for the divergence among all available contemporary and ancient genomes of African hunter-gatherers used to calibrate the model. In addition, it also accurately predicts the patterns of craniometric diversification across the continent from the Late Middle Pleistocene to the present. Finally, we show how the climate-driven changes in population sizes and connectivity are congruent with major patterns of archaeological and phenotypic diversification over the last 200,000 years across the African continent.

evolutionary biology↗

bioRxiv2025

Human life expectancies are still rising

Olshansky and collaborators have recently proposed that the era of continuous extension of human lifespans has finally come to an end1. By analysing thirty years of recent demographic data (1990-2020) from ten populations (the eight longest-lived nations, plus Hong Kong and the USA), they rejected the claims made by Oeppen and Vaupel at the start of the century2 (and more recently by Vaupel and collaborators3) that human longevity was still far from approaching an upper limit. However, on closer examination the results by Olshansky and colleagues seem to complement rather than directly challenge the radical life extension hypothesis. The reason is that the latter was based not on country-level demographic patterns but instead on a best-practice life expectancy trend resulting from the succession of annual world-leading populations. Here we present an update based on data from the last two decades that confirms Oeppen and Vaupels original insights and demonstrates that both female and male lifespans continue to linearly increase at a global scale. This remarkably long trend observed since 1840 remains at odds with our expectation that human lifespans must at some point hit a biologically imposed ceiling.

physiology↗

bioRxiv2025

Sexual division of labour shapes hunter-gatherer spatial ranges

Mobility lies at the adaptive core of the hunter-gatherer foraging niche, and has shaped the cultural and genetic evolution of our species. Yet, the specific drivers and consequences of mobility are still debated. Here we analyse the lifetime mobility patterns of 776 Mbendjele BaYaka hunter-gatherers from five regions in the northern Republic of Congo, revealing pronounced gender differences in spatial behaviour. While men expand their spatial ranges from adolescence to adulthood, womens ranges remain stable. We find evidence for a sexual division of labour underpinning these patterns, with mens greater mobility driven by subsistence activities such as hunting or exploratory trips away from camps, and womens mobility mostly driven by gathering closer to their residential location. Our findings challenge traditional assumptions of patrilocality, suggesting that men travel further due to their spatial separation from kin. Larger spatial ranges are associated with increased reproductive success for both genders, suggesting adaptive benefits of mobility in accessing resources, social networks, and potential mates. By linking individual behaviors to broader movement dynamics, our study deepens our understanding of gendered mobility in humans and highlights its significance to social structuring in our species and its evolutionary consequences.

evolutionary biology↗

bioRxiv2023

Population interconnectivity shapes the distribution and complexity of chimpanzee cumulative culture

While cumulative culture is a hallmark of hominin evolution, its origins can be traced back to our common ancestor with chimpanzees. Here we investigate the evolutionary origins of chimpanzee cumulative culture, and why it remained incipient. To trace cultural transmission among the four chimpanzee subspecies, we compared between-population networks based on genetic markers of recent migration and shared cultural traits. We show that limited levels of interconnectivity favored the emergence of a few instances of cumulative culture in chimpanzees. As in humans, cultural complexification likely happened in steps, with between-community transmission promoting incremental changes and repurposing of technologies. We propose that divergence in social patterns led to increased between-group mobility in Homo, propelling our lineage towards a trajectory of irreversible dependence on cultural exchange and complexification. One-Sentence SummaryPopulation interconnectivity through migration explains the origins of chimpanzee cumulative culture and why it remained incipient

evolutionary biology↗

bioRxiv2022

Hunter-gatherer oral microbiomes are shaped by contact network structure

Ancestral humans evolved a complex social structure still observed in extant hunter-gatherers. Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Comparisons of microbiome composition showed that the Agta are more similar to Central African Bayaka hunter-gatherers than to neighboring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that interaction networks covering large areas, and their strong links between close kin, spouses, and even unrelated friends, can significantly predict bacterial transmission networks across Agta camps. Finally, more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes, which are predominantly pathogenic, were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

microbiology↗

bioRxiv2022

The making of the oral microbiome in Agta hunter-gatherers

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analyzed the oral microbiota of the Agta, a hunter-gatherer population where part of its members is adopting an agricultural diet. We show that age is the strongest factor modulating the microbiome, likely through immunosenescence as there is an increase of pathogenicity with age. Biological and cultural processes generate sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggests that shifting from a fish/meat to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial, and shaped by various ecological and social factors that modify the oral environment.

microbiology↗

bioRxiv2021

Population inter-connectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers

The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density is explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions, as commonly assumed. We also predict hunter-gatherer presence across Central Africa over the past 120,000 years using paleoclimatic reconstructions, which were statistically validated by dated archaeological sites. Finally, we show that genomic estimates of separation times between CAHG groups match our ecological estimates of periods favouring population splits, and that recoveries of connectivity would have facilitated subsequent gene-flow. Our results reveal that CAHG stem from a deep history of partially connected populations. This form of sociality allowed the coexistence of relatively large effective population sizes and local differentiation, with important implications for the evolution of genetic and cultural diversity in Homo sapiens.

evolutionary biology↗