Biology subjects

Manica, A.

Publications and source records attributed to Manica, A..

At least 19 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

From margins to mainstream: restoration of riparian margins to support oil palm sustainability in modern and future climates

Palm oil is the worlds leading vegetable oil, with production continuing to expand, particularly across Southeast Asia. Within established plantations, conserving and restoring riparian margins can reduce erosion, improve connectivity, and support biodiversity. Simultaneously, climate change is increasing thermal stress within tropical agricultural landscapes, raising the potential importance of riparian buffers as microclimatic refugia, although this has not previously been evaluated. The Riparian Ecosystem Restoration in Tropical Agriculture (RERTA) Project is a long-term Before-After Control-Impact experiment established within oil palm plantations in Riau, Indonesia, to evaluate alternative riparian restoration strategies following plantation replanting. Treatments included passive restoration (retaining mature oil palms and allowing natural regeneration), active restoration (enrichment planting with six native tree species), and a control (replanting immature oil palms to the river edge). Six years after restoration, we assessed vegetation structure using terrestrial laser scanning and thermal stability using temperature loggers and thermal imaging. We also evaluated the long-term temperature buffering capacity of each treatment under current and projected climates using CHELSA climate data and downscaled outputs from multiple General Circulation Models under Shared Socioeconomic Pathway scenarios for 2045 and 2085. Active restoration produced greater structural complexity, a more closed canopy, and cooler, more thermally stable conditions than passive restoration and control treatments. Restored margins also contained significantly more cool surface microhabitats, reducing thermal extremes under both current and future climate scenarios. Our findings demonstrate that active restoration of riparian margins can enhance thermal buffering and create microclimatic refugia for biodiversity within tropical oil palm landscapes. As agricultural intensification and climate change continue to reshape tropical ecosystems, restoring structurally complex riparian vegetation will be critical for sustaining biodiversity and the ecosystem services upon which agricultural production depends.

ecology↗

bioRxiv2026

Plague-driven selection enriched familial Mediterranean fever mutations in Armenia

The discovery that positive selection due to resistance to malarial infection maintained the prevalence of sickle cell and other disease alleles was a landmark in evolution, genetics and epidemiology. Mutations in the MEFV gene causing familial Mediterranean fever with high frequency in Eastern Mediterranean populations give the only other strong candidates for a similar process. Here we estimate a pathogenic MEFV mutation burden in Armenians with a carrier rate of ~41%: a worldwide maximum. By combining these data with regional ancient MEFV genotypes spanning more than 60 centuries, we establish that the allele frequencies of three mutations M694V, M680I, and V726A underwent recent rapid increases, indicating positive selection with an onset consistent with the first Yersinia pestis plague pandemic, ~541 CE to 767 CE or even earlier in time, echoing functional data implying resistance to this infection as the selective agent. This extends to three the number of MEFV variants for which there is evidence for strong concurrent selection at this locus in the Eastern Mediterranean, making it unlikely that this geographic peak resulted from chance alone. Although bubonic plague was extremely widespread, the restricted geography of this selection points toward the Eastern Mediterranean as a longstanding enzootic centre with continuous recycling of outbreaks.

genomics↗

bioRxiv2026

Parallel phenotypes underpinned by different genes in the visual system of two trans-isthmian coral reef fish species pairs

Understanding the genetic basis of adaptation in natural populations to changing environmental conditions is challenging. The relatively simple genotype-to-phenotype relationship between opsin genes and visual pigments offers a particularly informative model to explore the molecular mechanisms underpinning adaptive phenotypic change in natural populations. Here we leveraged the natural experiment provided by the tectonic closure of the Central American seaway that created allopatric, sister taxa in multiple, independent lineages of marine organisms and exposed them to distinct underwater light environments: either the more turbid Tropical Eastern Pacific (TEP), or the spectrally broader Caribbean Sea. Using two species pairs of planktivorous teleosts, the Azurina multilineata/A. atrilobata damselfish and the Cephalopholis (Paranthias) furcifer/C. colonus groupers, we explore to what extent visual sensitivity converged to similar adaptations in response to similar foraging strategies and shared underwater light in each marine basin. We found that the compression of the underwater light field towards the central portion of the spectrum from Caribbean to TEP waters is reflected in similar shifts towards the centre of the light spectrum in overall single and double cone sensitivities in both families. Both TEP species have single (short-wavelength) cone sensitivities shifted to longer wavelengths and double (long-wavelength) cone sensitivities shifted to shorter wavelengths, compared to their Caribbean counterparts. These parallel shifts in visual sensitivities observed in response to shared underwater light environments are accomplished by different underlying opsin gene toolsets in the two lineages. Similarly, expression changes in pathways associated with the visual system revealed limited parallelism at the molecular level.

evolutionary biology↗

bioRxiv2026

Fine-scale population structure within and among Malagasy societies

The population of Madagascar exhibits a globally unique combination of African and Asian genetic ancestries. Previous studies have described the admixture history of Madagascar at island-wide scales [1,2], but less focus has been paid to fine-scale population structure across the island. We present new genome-wide genetic data from 192 individuals sampled across five regions of Madagascar. We identify population structure at extremely fine spatial scales ([~]10 km) among the Merina of the central highlands. By analysing subpopulations separately, we found one Merina group exhibited similarity to coastal populations in f4 ratios, estimated admixture dates, and pairwise FST distances, while another group was similar to other highland individuals in the same measures. This fine-scale substructure is likely associated with historical coastal-to-highland migration during the 18th and 19th centuries. In contrast, we also observe macro-scale structure in estimated timing of admixture across the island, with southeastern coastal groups exhibiting the earliest estimated admixture timings, and northern groups exhibiting the latest. This pattern corroborates previous results [1,2], and may suggest differing histories of admixture timing among Malagasy populations. Our results emphasise the importance of deep micro-geographic sampling to complement macro-scale analysis when characterising demographic history.

genetics↗

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

The origins and molecular evolution of sperm

Sperm is a nearly universal cell type among animals, yet its evolutionary origins remain unclear. Using comparative proteomics and phylogenomics across 32 species, we reconstruct the 700+ million year evolutionary history of sperm to define the Last Universal Common Sperm (LUCS), a conserved core of 301 gene families enriched in motility and energy metabolism. We found that most of the LUCS toolkit was developed in filozoan unicellular ancestors approximately 400 Ma before animals, revealing sperm as a reconfigured legacy from our unicellular past rather than an invention of multicellularity. Sperm shows a within-cell evolutionary gradient, both spatial and temporal, where ancient proteins dominate the tail, while younger innovations concentrate in the head. The oldest sperm components are disproportionately associated with human infertility, establishing an empirical bridge between evolutionary depth and clinical relevance. Together, our findings reveal how evolutionary history is inscribed within a single cell and can guide clinical insights.

evolutionary biology↗

bioRxiv2025

Comparative genomic analyses of trans-ithmanian reef fishes reveals different molecular targets of environmental adaptation in different families.

The extent to which selection acts upon the same molecular targets when faced with the same environmental changes has important implications for our understanding of the repeatability and predictability of evolutionary processes. Replicated natural experiments are well positioned to provide insight, however often these involve closely related species or populations of the same species. Given that the similarity of genetic background makes the same molecular change more likely, it is essential to evaluate the extent to which molecular parallelism occurs in more distantly related species. The rise of the Isthmus of Panama presents an ideal natural experiment to investigate the prevalence of parallel molecular changes in distantly related lineages exposed to the same environmental regimes of temperature, salinity and primary productivity in the two newly formed oceans. Here, we generate high-quality reference genomes for two replicate pairs of geminate reef fishes, one in the family Pomacentridae and one in the Serranidae. Comparative analyses of positive selection in protein-coding genes and of gene family evolution revealed multiple signals of potentially adaptive divergence between geminate species in response to environmental regime. Common targets of selection between families included MAPK signalling (MAP3K10), solute transport (SLC46A2) and reproduction (ZPL3L), as well as expansions in immune and MAPK related gene families. Overall, however, we found minimal evidence of parallelism between families either at the gene level or when considering higher functional categories. Our findings suggest that phylogenetic constraints may limit the levels of molecular parallelism in distant lineages even when faced with comparable selective pressures. Significance StatementUnderstanding the extent to which species exposed to similar environmental conditions may adapt using similar genetic solutions has important implications for our understanding of evolutionary processes and how we may expect species to adapt in the future. However, systems where multiple, independent lineages are faced with the same shift in conditions are rare. The rise of the Isthmus of Panama provides a unique, natural experiment where multiple marine species have been divided and exposed to radically different environmental conditions. Here, we generate genomes for separated species in two distantly related families of reef fishes and compare genome-wide patterns of divergence. Our analyses identified signals of selection in protein-coding genes and shifts in gene family size consistent with adaptation to the distinct environments, however the specific genes and pathways involved predominantly differed between the families, revealing that, even under shared selective pressures, molecular mechanisms may differ across more distant lineages.

evolutionary biology↗

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

Palaeoproteomic and genetic insights into millennial-scale dairy consumption in Armenia

Dairy products are a key component of the diet in Armenia today, yet the origins of milk consumption, its historical development, and genetic adaptations related to milk digestion in the region remain understudied. Here, we investigate the co-evolution of dairying practices and lactase persistence in Armenia through combined palaeoproteomic and genetic analyses spanning from prehistory to the present. Our palaeoproteomic results provide direct evidence for milk consumption in prehistoric Armenia and, in conjunction with existing regional data, indicate that dairying was an established component of the South Caucasus subsistence economy from at least the late fourth millennium BCE. We found evidence of milk consumption from multiple species across archaeological periods, with cattle milk representing the earliest confirmed evidence from the Chalcolithic period. Notably, milk proteins were predominantly recovered from high-altitude sites, suggesting that dairy consumption served as an adaptive strategy for harsh highland environmental conditions. In contrast to the widespread evidence for milk consumption, our genetic findings indicate that the lactase persistence-associated variants never reached high frequencies throughout Armenian prehistory. This pattern suggests that the relatively low frequency of lactase persistence may reflect a predominant cultural adaptation to the fermentation of dairy products, which reduces lactose content and enables dairy use even in genetically lactose-intolerant populations.

evolutionary biology↗

bioRxiv2025

Community ecology dynamics on reefs in Fiji are dependent on soft coral density and depth

Some soft corals (order Alcyonacea) have the potential to increase in prevalence on tropical coral reefs as the severity of anthropogenic climate change increases. While soft corals are therefore an increasingly important component of reef ecosystems, little is known about their ecological role on coral reefs and their influence on community dynamics and diversity. We used Bayesian Network Inference to identify the relationships among benthic taxa across sites with varying degrees of soft coral dominance on the Great White Wall, Fiji, and then employed spatial point process analysis to reveal the ecological processes behind these associations. We found that depth was the dominant driver of community dynamics, and that white Nephtheidae soft corals were negatively associated with scleractinian corals and positively associated with algae due to a facilitative mutualism - possibly due to soft corals reducing grazing pressure. Our results show distinctions in reef benthos and ecological dynamics between scleractinian- and soft coral-dominated reefs. We found that diversity levels were significantly lower on soft coral than scleractinian reefs, potentially highlighting the risk of a loss in benthic diversity on reefs where soft corals replace scleractinians.

ecology↗

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

tidypopgen: Tidy Population Genetics in R

As genome-wide data has become increasingly available, software libraries for their analysis have proliferated. While new tools for downstream analyses are constantly emerging, existing workflows are hindered by inefficiencies. Switching between coding languages and object types in the early stages of pipelines wastes researchers time, impedes reproducibility, and creates opportunity for error. To confront these obstacles, we introduce tidypopgen, a comprehensive R package for population genetic analysis of biallelic SNP data. Genotype data can be read, filtered, and analysed within a single environment, without the need for prior data cleaning or setup with other software. tidypopgens gen_tibble object structure makes analysis efficient and intuitive, while standardised tidy grammar makes data manipulation clear. Functionality within tidypopgen supports cleaning and merging datasets, basic descriptive statistics, multivariate analysis, clustering algorithms, and F-statistics, as well as integrating with existing tools for population genetic analyses in R. We use the Human Genome Diversity Project SNP dataset (Li et al., 2008) to show that a basic population genetic workflow can be executed in under 25 lines of code in a single environment using one file set, without the need to write superfluous outputs or change directories. By supporting data assembly through to data analysis, tidypopgen significantly streamlines workflows without compromising speed or functionality.

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

Recolonisation strategies of early animals in the Avalon (Ediacaran 574 - 560 Ma)

The first geographically widespread metazoans are found in the Avalon assemblage (Ediacaran; 574 - 560 Ma). These early animals were regularly disturbed by sedimentation events such as ash flows and turbidites, leading to an apparent "resetting" of communities. However, it is not clear how biological legacies - remains or survivors of disturbance events - influenced community ecology in the Avalon. Here, we use spatial point process analysis on 19 Avalon palaeocommunities to test whether two forms of biological legacy (fragmentary remains of Fractofusus and surviving frondomorphs) impacted the recolonisation dynamics of Avalon palaeocommunities. We found that densities of Fractofusus were increased around the Fractofusus fragments, suggesting that they helped to recolonise the post-disturbance substrate, potentially contributing to the Fractofusus dominance found in 8 of the 19 palaeocommunities. However, we found no such effects for survivor fronds. Our results suggest that the evolution of height was for long-distance dispersal rather than local recolonisation. In modern deep-sea environments, there is a trade-off between local and long-distance dispersal, and our work demonstrates that this differentiation of reproductive strategies had already developed in the early animals of the Avalon.

ecology↗

bioRxiv2025

The influence of reproductive mode on resource competition and diversity patterns in Ediacaran early animal communities

The appearance of the oldest known animals during the late Ediacaran ([~]574 million years ago [Ma])1-4 was followed by a phase of little change5. This period, which lasted [~]14 million years, ended with a burst of rapid diversification known as the Ediacaran "Second Wave". The reasons for these diversity patterns are poorly understood. Here we investigate how reproductive mode mediated community dynamics, and in turn macroevolutionary change, in the Ediacaran. We show that widespread reproduction via stolon (namely via filaments connecting clones) in the first animals limited intra-specific competition among neighbours, leading to inter-specific competition acting at smaller-spatial scales than intra-specific competition, a phenomenon called heteromyopia6. Heteromyopia enables co-existence of sub-optimal competitors because the dispersal limitation of the dominant species means that they do not inhabit all the optimal habitat, so that lesser competitors can still exist within the same community, operating under reduced selection pressure. We explored the consequences of this dispersal limitation on community diversity using Approximate Bayesian Computation to estimate the posterior distributions of dispersal with a spatially explicit model fitted to the three Ediacaran assemblages and showed that the change from stoloniferous to sexual reproduction that coincided with the Second Wave could explain the sudden increase in alpha diversity observed in the fossil record. We conclude that widespread asexual reproduction via stolon likely constrained early animal evolution, limiting diversification until the onset of mobility and widespread sexual reproduction7-9.

paleontology↗

bioRxiv2024

The environmental context of the Middle-to-Late Stone Age Transition in eastern Africa: seasonality as a key factor

In the transition between the Middle Stone Age (MSA) and the Late Stone Age (LSA) in eastern Africa, the archaeological record shows a gradual and asynchronous decline in MSA features and an increase in LSA characteristics. A link between this pattern and climatic variations has not yet been tested in the region using lithic attribute analysis. To investigate that, we integrated technological data of blades and bladelets from eastern African contexts (Marine Isotope Stages 5-1) with large-scale paleoclimatic reconstructions. A principal component analysis (PCA) finds the first component (reflecting artifacts dimensions) significantly correlating with time. This highlights a progressive reduction in size over time, a trend that has already been suggested for the MSA-LSA transition. The second principal component reflects artifact shape and shows a significant correlation with the marked aridity of the dry season (a common proxy for seasonality in tropical regions), with higher specialization observed in more humid areas. Based on this, we propose a new model where more variable blades reflect greater versatility in foraging strategies as adaptation to environments that become more challenging during part of the year. On the other hand, when it rains more during the dry season and differences through the year are milder, a more specialized toolkit with thinner, longer elements would emerge from refining and adapting to uniform and predictable situations and challenges.

evolutionary biology↗