Biology subjects

Padilla-Iglesias, C.

Publications and source records attributed to Padilla-Iglesias, C..

10 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

Climate Shaped the Global Population Structure of Leopards and their Extinction in Europe

Environmental change is often invoked as a key force shaping species evolution and demography, but quantifying its role is challenging. Leopards (Panthera pardus), a widely distributed generalist species, provide an ideal case for studying the role of the environment. The population dynamics of African and Asian leopards differ dramatically, with near panmixia in Africa versus a strong structure and eight subspecies in Asia. Fossil records show that a population in Europe disappeared after the Last Glacial Maximum (LGM), further pointing to complex range dynamics in Eurasia. In this study, we explicitly test the role of climate in shaping leopards population dynamics across the continents, by quantitatively combining paleoclimatic, demographic, and genetic simulations over the last 450 thousand years. Using an Approximate Bayesian Computational framework, we show that the genetic structure differences between Africa and Asia can be explained by distinct historical climatic conditions in these two continents: most of sub-Saharan Africa and parts of Southeast Asia exhibited a stable range without geographical barriers, while other areas such as Morocco, Afghanistan and Northeast Asia showed expansion and extinction cycles during glacial and interglacials. We further model population dynamics in Europe and validate it against fossil and radiocarbon dates records. We find that European populations were likely fragile, with extinctions repeatedly predicted over multiple glacial cycles, indicating that climate change possibly led to the extinction of the European subspecies following the LGM. Notably, we found that climate during the Holocene should have allowed a more recent recolonisation that did not happen, indicating other factors such as human presence might have blocked it.

zoology↗

bioRxiv2025

tidygenclust: Clustering for Population Genetics in R

BackgroundPopulation structure analysis is crucial for evolutionary research and medical genomics. Clustering methods, broadly categorized as model-based (e.g. ADMIXTURE) or non-model-based (e.g. SCOPE), differ in their methodology and computational efficiency. Recently, fastmixture, a model-based approach, has improved scalability and performance, while replicate alignment tools, such as Clumppling, extend previous methods by also aligning the modes across K values. However, all the existing tools are standalone and generate numerous untracked text files, as well as offering limited plot customisability. ResultsWe introduce an R package, tidygenclust, which brings the functionalities of the original ADMIXTURE, fastmixture and Clumppling software into R, enabling a streamlined and integrated workflow. By integrating with tidypopgen, a package designed to handle large SNP datasets, these new tools maintain metadata, simplify data handling, and produce results as customisable ggplot2 objects for flexible visualisation. ConclusionsThe R package tidygenclust advances population genetic analysis by combining computational efficiency with reproducible workflows and user-friendly plotting. The source code and instructions can be accessed on https://github.com/EvolEcolGroup/tidygenclust.

bioinformatics↗

bioRxiv2025

Malaria shaped human spatial organisation for the last 74 thousand years

The mechanisms driving the spatial organisation of early human societies in Africa are typically addressed through climate variables 1-3. However, genetic and archaeological studies have also suggested diseases as a major source of selection in the Pleistocene. Here, we explore whether P. falciparum-induced malaria, a major world disease, drove habitat choice in human societies between 74 and 5 thousand years ago (kya). Using species distribution models of three main mosquito complexes with palaeoclimatic reconstructions and combining the results with epidemiological information, we estimated an index of malaria transmission risk in sub-Saharan Africa through time. We then correlated it with an independent reconstruction of the human niche over the same time period and region. Our results show that humans strongly avoided or were unsuccessful in potential malaria hotspots. The effects of these choices shaped human demography for the last 74 kya, and likely much earlier, by fragmenting human societies over time and contributing to the formation of modern population structure. Our results highlight the importance of considering disease distributions when modelling estimates of past human demography, demonstrating that factors beyond climate underlay patterns of human habitat choice, exchange, and dispersal. Sentence summaryMalaria shaped human habitat choice, exchange, and dispersal since the late Pleistocene in sub-Saharan Africa.

evolutionary biology↗

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

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↗

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↗

bioRxiv2021

Hunter-gatherer foraging networks promote information transmission

Central-place foraging, where foragers return to a central location (or home), is a key feature of hunter-gatherer social organization. Central-place foraging could have significantly changed hunter-gatherers use of space and mobility, and altered social networks and increased opportunities for information exchange. We evaluated whether central-place foraging patterns facilitate information transmission and considered the potential roles of environmental conditions and mobility strategies. We built an agent-based central-place foraging model where agents move according to a simple optimal foraging rule, and can encounter other agents as they move across the environment. They either forage close to their home within a given radius or move the location of their home to new areas. We analyzed the interaction networks arising across different environments and mobility strategies. We found that, at intermediate levels of environmental heterogeneity and mobility, central-place foraging increased global and local network efficiencies as well as the rate of contagion-based information transmission (simple and complex). We also assessed the effect of population density on the resultant networks and found that central-place mobility strategies can further improve information transmission in larger populations. Our findings suggest that the combination of foraging and movement strategies, as well as the underlying environmental conditions that characterized early human societies, may have been a crucial precursor in our species unique capacity to innovate, accumulate and rely on complex culture.

evolutionary biology↗