Philosophical Transactions of the Royal Society B
● The Royal Society
Preprints posted in the last 90 days, ranked by how well they match Philosophical Transactions of the Royal Society B's content profile, based on 51 papers previously published here. The average preprint has a 0.20% match score for this journal, so anything above that is already an above-average fit.
Arner, A. M.; McCabe, T. C.; Seyler, A.; Zamri, S. N.; A/P Tan Boon Huat, T. B. T.; Tam, K. L.; Kinyua, P.; John, E.; Ngoci Njeru, S.; Lim, Y. A.; Gurven, M.; Nicholas, C.; Ayroles, J.; Venkataraman, V. v.; Kraft, T. S.; Wallace, I. J.; Lea, A. J.
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ObjectivesEffective communication about genetics concepts is essential for collaborative anthropological genetics research. However, communication can be challenging because many ideas are abstract and may be especially unfamiliar to communities with limited access to formal education. Indeed, there are no widely adopted models for communicating such information, nor a clear understanding of the social factors that may shape participant engagement. Here, we conducted a qualitative and quantitative, community-driven study to understand how illustrations can be useful to support concept sharing with two Indigenous groups--the Orang Asli of Peninsular Malaysia and the Turkana of Kenya. MethodsWe used a two phase approach to create and evaluate how illustrations can bolster communication about genetics concepts. First, we created images illustrating answers to frequently asked questions about genetics, iteratively updating the illustrations based on participant feedback. Second, we conducted 92 interviews to evaluate the finalized illustrations effectiveness. Finally, we analyzed the interview data using thematic analyses, multivariable modeling, and multiple correspondence analyses to identify patterns in participant understanding and feedback, including age, sex, market integration, and schooling. ResultsParticipants reported high interest in genetics research (92%) and broadly positive perceptions of the illustrations. Familiar, locally-grounded imagery was preferred and associated with greater perceived clarity, while more technical illustrations were more frequently reported as confusing. Quantitative analyses showed strong internal consistency across measures of engagement and understanding, with modest variation by degree of market-integration, schooling, and sex. DiscussionOur findings demonstrate that community-specific visualizations, co-developed through iterative feedback, can effectively support engagement with genetics research in participant communities.
Hannah, J.; Di Liberto, G. M.
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Trust is a critical component of human communication, providing a foundation for understanding, information exchange, and social coordination. Much of the research on trust in speech communication has focused on how vocal characteristics impact perceived trustworthiness. However, little is known about how trust in a speaker affects the neural processing of speech. Here, we demonstrate a two-stage experimental framework to study that question using non-invasive EEG. First, participants engage in a trust-building stage, where they play an investment game with fictional characters, each paired with a distinctive voice and trustworthiness level (i.e., frequency and magnitude of lies). Next, participants engage in a story-listening stage, in which they are presented with stories from the same characters. Data acquired from twenty young adults confirm a statistically significant correlation between the perceived and actual trustworthiness of the fictional characters. Cortical speech tracking was quantified using a temporal response function (TRF) analysis on the EEG data. We found that the trustworthiness established during the trust-building stage influenced the cortical tracking of speech in the subsequent story-listening stage, with lower trustworthiness corresponding to a stronger cortical tracking of speech. Interestingly, trustworthiness selectively modulated tracking strength, with no statistically significant changes in how language is represented across space and time.
Halperin, J.; Perlman, S.; Shemesh, S.; Harris, K. D.; Greenbaum, G.
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Gene drives, genetic constructs that can spread deleterious alleles in wild populations, have the potential to address some of the major pressing challenges of the Anthropocene such as invasive species, spread of disease vectors, and agricultural pests. However, responsible and effective deployment of gene drive requires taking into account the complex nature of real-world population connectivity networks. In particular, it is unclear how the topological position of the deployment site affects the spread process and its final outcome. Here we develop a framework for modeling gene drive spread in population connectivity networks, and study the eco-evolutionary dynamics of gene drive spread under complex population structures. We investigated the relationship between the position of the deployment site in the topology of the network and whether the gene drive is eventually lost, fixed, or maintained at an intermediate frequency. We identified network centrality measures of deployment sites that are highly correlated with the outcome of deployment for different gene drive designs and across diverse network topologies. We also show that there is a trade-off between the time-to-fixation and the final outcome, implying that multiple centrality measures of the deployment site would need to be considered when aiming to achieve rapid and successful population control using gene drives.
Guillemet, M.; Lehtinen, S.
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The evolutionary dynamics determining whether an antimicrobial resistance (AMR) gene resides on a plasmid or a chromosome are critical to understanding the spread of resistance. While theoretical models often predict that beneficial traits should ultimately integrate into the more stable chromosome, contemporary genomic data frequently shows a strong enrichment of resistance genes on mobile, yet costly and less stable plasmids. Here, we propose that the widespread plasmid-mediated resistance observed today may not represent a stable evolutionary equilibrium, but rather a snapshot of an ongoing process. Using a stochastic multi-strain model, we explore the role of strain diversity as a determinant of the timescale of this process. We suggest that the population structure of the bacterial host species, maintained by balancing selection, acts as a substantial barrier to the selective sweep of vertically transmitted chromosomal genes. Because horizontal transmission allows conjugative plasmids to readily cross these strain boundaries, our model indicates that plasmid-borne resistance can transiently dominate the population before chromosomal integration takes over, and that this transient dominance can last for decades. We illustrate these predictions by analysing antimicrobial resistance gene location in three common opportunistic gut pathogens. Furthermore, we show how extending the model to include co-selection between resistance genes on multi-drug resistance plasmids can lead to more complex dynamics that transiently reverse this plasmid-to-chromosome trajectory. Overall, our findings highlight how bacterial population structure can dictate the evolutionary trajectory of beneficial genes, suggesting that the current distribution of AMR genes between chromosome and plasmids is a prolonged transient state rather than a static endpoint.
Glover-Kapfer, P.; Fowles, G.; Dougan, G.; McCarthy, K.
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Wildlife crossing infrastructure is promoted to restore connectivity for fragmented populations, but its effectiveness at enabling natural recolonisation remains untested. We tested this using a spatially explicit agent-based model parameterised with GPS telemetry data from bobcats (Lynx rufus) in New Jersey, USA. By integrating movement behaviour, stochastic demography, habitat suitability, and traffic-dependent mortality risk, we simulated 50-year recolonisation dynamics across a highly urbanised landscape. Despite extensive unoccupied suitable habitat, natural recolonisation completely failed across all scenarios, with vehicle-induced mortality during dispersal acting as the primary limiting factor and turning the matrix into a demographic sink. Even an idealised mitigation scenario in which mortality at high-mortality crossings was reduced to zero failed to produce a self-sustaining population. Although dispersal increased, individuals at the recolonisation front remained too sparse to overcome the mate-finding Allee effect. Sensitivity analysis confirmed that the recolonisation-failure result is robust to {+/-}50% variation in per-crossing mortality and {+/-}25% variation in disperser survival. Restoring structural connectivity is not, in itself, a sufficient intervention for recovering low-density carnivore populations facing a high-mortality matrix. Instead disperser survival and local density at the recolonisation front are the rate-limiting determinants. In such systems translocation rather than crossing-structure investment is more likely to result in recolonisation success.
Sriwichai, N.; Feriau, L.; Tongyoo, P.; Noda, Y.; Gyoji, H.; Noisagul, P.; Goto, S.; Steinberg, D.; Wangsanuwat, C.
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This dataset arises from a multilingual survey of AI use among participants and community members in the DBCLS BioHackathon 2025 in Japan. The questionnaire, offered in English, Japanese, and Thai, asked about how often respondents use AI tools, what they use them for, obstacles they encounter, institutional support, satisfaction, and concerns. Additional items captured role, institution type, work country, and other demographics, totaling 105 responses. The dataset includes both raw anonymized responses and a cleaned, standardized English-only version suitable for quantitative analysis, along with the full questionnaire, a data dictionary for cleaned dataset, and a translation lookup table. Free-text answers were screened and redacted to remove URLs, names, and other potentially identifiable information. Together, these materials provide a community-level view of AI practice in genomics, bioinformatics, software development, and related areas, and can support work on AI adoption, policy, and methods for analyzing survey data on AI use in science.
Mlynarek, J.; Heard, S. B.; Mammola, S.
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If youve ever complained about a species name thats a mouthful--say, the soldier fly Parastratiosphecomyia stratiosphecomyioides or the myxobacterium Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis--youre in very good company. But could the readability of binomial scientific names cause more than complaints? Could it influence how much species are studied and talked about? We examined a random sample of 3,019 species names spanning 29 phyla/divisions. We tested whether name length and reading difficulty are associated with species representation in the scientific literature (measured via literature mentions) and their visibility to the public (measured via Wikipedia pageviews). Both species name traits showed significant negative relationships with literature mentions and Wikipedia reads. Increasing name length from 10 to 30 characters is associated with a 66% decrease in expected mentions and a 65% decrease in Wikipedia reads, while shifting from the most to the least readable name in the dataset corresponds to 53% and 76% decreases. These patterns are consistent with something familiar: the fickleness of human attention, responding to features of the world that are far from rational. While creativity in naming is a cherished part of taxonomy, a touch of orthographic restraint may ultimately benefit both science and the species themselves--especially among understudied uncharismatic taxa.
Quinn, L.; Jeglinski, J. W. E.; Auhage, S.; Balmer, D.; Bringsvor, I. S.; Burton, E.; Castenschiold, J. H.; Christensen-Dalsgaard, S.; Danielsen, J.; Dierschke, J.; Ezhov, A. V.; Gudmundsson, G. A.; Hart, T.; Jessopp, M.; Jones, R.; Krasnov, Y. V.; Lorentsen, S.-H.; Palsdottir, A. E.; Provost, P.; Purdie, A.; Morgan, G. D.; Emma, M.; Olsen, B.; Strom, H.; Tierney, D. T.; Wilson, L. J.; Wanless, S.
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Northern gannets (Morus bassanus) have been regarded as a seabird success story, due to population increases throughout the 20th and 21st century contrasting with global seabird declines. However, in 2022 gannets experienced a severe outbreak of High Pathogenicity Avian Influenza (HPAI) across their global distribution, leading to an urgent need to reassess their population status. This study presents breeding gannet census numbers for 2023/24 from all colonies across the North-East Atlantic metapopulation (Great Britain, Ireland, the Channel Islands, Iceland, Norway, the Faroe Islands, France, Germany, Russia). Gannet numbers decreased by 17% across the North-East Atlantic metapopulation between the 2013/14 and 2023/24 census from 414,598 to 345,854 apparently occupied sites (AOS), a global decrease of at least 13%. The bulk of the reduction in AOS was driven by the largest colonies (>10,000 AOS) each losing tens of thousands of AOS. These figures likely underestimate the impact of the HPAI outbreak worldwide, since most colonies will have increased between the last census in 2013/14 and the 2022 HPAI outbreak, and the Canadian breeding population was last counted pre-HPAI outbreak. Scotland still holds the largest proportion of both the North-East Atlantic metapopulation (59%), and the world population (46%), while Great Britain, Ireland and the Channel Islands together hold 83% of the North-East Atlantic metapopulation and 64% of the world population. This study not only presents an updated population census for gannets in the North-East Atlantic but illustrates the large-scale impacts of a disease outbreak on a seabird species across its global range and highlights the importance of more regular census efforts to better quantify the demographic consequences of such events.
Glaus, K.; Benestan, L. M.; Brunnschweiler, J.; Devloo-Delva, F.; Appleyard, S.; Rico, C.
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Understanding relatedness in sharks is challenging due to uncertainty in distributions, low population densities and difficulties in sampling across life stages. In Fiji, bull sharks (Carcharhinus leucas), with an effective population size estimate of [~]258, aggregate at the Shark Reef Marine Reserve (SRMR), but gravid females disperse at the end of the year to give birth in adjacent rivers. Questions remain regarding reproductive connectivity, female returns across years, and kinship structure. Using population genomics on 296 bull sharks across age classes (neonates, young-of-the-year, juveniles, and adults) collected over a decade at the SRMR and in three adjacent rivers, we assessed familial connections. Direct genetic links, including first- and second-degree relationships, connected SRMR adults with young age classes in the Navua and Rewa rivers, providing evidence of reproductive connectivity. Within rivers, genetic similarities across cohorts revealed reproductive philopatry. Remarkably, several individuals sampled years apart were assigned to the same sire-dam pairs, indicating repeated pairings across breeding seasons. However, the few related links detected between the SRMR and the rivers may reflect incomplete sampling. Altogether, bull shark reproduction in Fiji seems influenced by reproductive philopatry and repeated pairings, suggesting added complexity in their reproductive behaviour.
McPherson-McNato, M.; Undurraga, E.; Seidle, A.; Honeycutt, O.; McDermott, J. H.
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Pitch is a building block of speech and music, but the extent to which pitch perception is shared across cultures is unclear. Evidence from Western participants suggests that pitch perception relies on multiple representations. For instance, harmonic tones are easier to discriminate in noise than inharmonic tones despite comparable discrimination in quiet, suggesting that different representations are used in noise and quiet. We tested whether these effects are present cross-culturally, comparing participants from the US and a Bolivian Amazonian Indigenous community (Tsimane). Participants heard two-note melodies and reproduced the melody by singing. Tones were either harmonic or inharmonic and were presented in noise or quiet. Both groups exhibited two characteristics of pitch perception previously seen in US listeners: the direction of pitch changes could be reproduced with equal accuracy for harmonic and inharmonic tones in quiet but was better for harmonic than inharmonic tones in noise. However, replicating previous work, Tsimane vocal reproductions were much less likely to be related to the absolute pitch or chroma of the stimulus notes, differing from the tendency seen in Western participants to match pitch and/or chroma. Pitch and chroma matching behavior were more prominent in a subset of Tsimane whose responses to a demographic survey suggested greater integration with global and Bolivian markets and culture. The results demonstrate that the basic structure of pitch perception is shared across cultures despite other differences in pitch-related behavior that are plausibly driven by culture-specific experience.
Madden, J. R.; Sage, R. B.; Wilde, J. A.
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Large-scale annual releases of pheasants Phasianus colchicus and their subsequent management for recreational shooting create various ecological impacts in the UK. While effects at release sites are fairly well understood, dispersing birds may influence areas farther away. If they enter ecologically important but sensitive protected areas (PAs), any negative impacts could be especially harmful. Using tracking data, from 766 birds across 10 sites, we estimated survival and dispersal of released pheasants and applied these patterns to gamebird release records near English PAs to gauge intrusion risk. Of 2,885 registered release sites, just over half lay within 2 km of a PA. A large number of shoots release relatively few birds while a small number release many birds. Thus, numbers expected to enter a particular PA likely depend both on the size of releases and proximity to the PA. We estimate that, at a national level, a maximum of between 525,000 and 784,000 pheasants might be found within PAs very soon after release, representing around 1.7% of all the pheasants released annually. This number declines over the months after release until in February, we estimate that there are between 131,000 and 196,000 pheasants (0.4% of the total release) might be found within PAs. The critical metric by which ecological damage might occur is their density within PAs. Mean densities soon after release averaged 12.0 birds/ha in PAs within 250 m of release sites. This density declined markedly both in time (as birds died) and space (as they moved further from the pen as potential areas increased). By November, densities in PAs 500-1000m from release sites peaked at 0.5 birds/ha, falling to 0.16 birds/ha in February. These estimated densities are around two orders of magnitude lower than those known to cause strong, lasting impacts within release pens. The results are subject to assumptions about movement behaviour, game management and bias in registration. Despite these constraints, considerable local variation exists, with a minority of high-volume release sites very near PAs posing the greatest potential ecological risk.
Berger, J.; Wittmann, M. J.
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The Allee effect is a phenomenon where individual fitness is reduced in small populations, for example because of mate-finding difficulties or increased predation. Allee effects matter in conservation biology because they can drive small populations to extinction. The severity of Allee effects can depend on traits such as mate-search rate and defense against predators. Many natural populations exhibit considerable intraspecific trait variation (ITV) in such traits, but most studies so far assume these traits to be constant. Thus the impact of ITV on populations with Allee effect is largely unknown. Here we create two individual-based stochastic models that simulate a small population experiencing either a mate-finding Allee effect or a predator-driven Allee effect. We analyze how ITV, trait inheritance, and mutation affect the proportion of surviving populations. Under the mate-finding Allee effect, higher ITV hindered population survival and increased Allee thresholds. This can be explained by Jensens inequality and the negative curvature of the mate-finding function. Under the predator-driven Allee effect, ITV effects were weak, but higher mutation standard deviations were beneficial, likely because they provided more substrate for selection to act on. We thus recommend to take into account ITV when dealing with threatened populations with an Allee effect.
Arrieta-Sagredo, I.; Blanco, B.; Caballero-Gaudes, C.; Carreiras, M.; Kalashnikova, M.
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Young children acquire language in environments where speech is often acoustically degraded, yet little is known about how developing brains adapt to reduced speech intelligibility. Using a combination of eye-tracking and functional near-infrared spectroscopy (fNIRS), we investigated young childrens attentional allocation to a speaking face at varying levels of speech intelligibility and the brain activity supporting this behaviour during development. Infants (8-10 months) and toddlers (27-30 months) viewed videos of a speaker in three conditions: producing clear speech, spectrally degraded (vocoded) speech, and silent (audio muted) speech. Visual attention to the speakers mouth increased when speech was degraded relative to clear speech in both age groups, indicating an early-emerging compensatory strategy. However, this shared behavioural response was supported by brain activity that differed by age. Degraded speech elicited greater recruitment of prefrontal regions associated with effortful listening, particularly in infants, whereas toddlers showed stronger engagement of posterior temporal regions implicated in audiovisual integration. In response to silent speech, there was no evidence for increased visual attention to the mouth compared to the clear speech condition, but there was reduced temporal activation and increased prefrontal brain responses, especially in infants. Together, these findings suggest that experience with audiovisual correspondences and linguistic maturity contribute to a more efficient processing of speech, particularly relevant when speech is degraded. By combining behavioural and neuroimaging measures, this study advances mechanistic accounts of audiovisual speech processing and provides insights relevant to populations experiencing spectrally degraded input, such as children using cochlear implants.
Rocchi, F.; Haukes, N. C.; van Opstal, A. J.; van Wanrooij, M. M.
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AO_SCPLOWBSTRACTC_SCPLOWVision can shape auditory perception, especially when visual cues occur at different times and locations than sounds. Simultaneous but spatially misaligned lights bias the perceived location of a sound--a phenomenon known as the ventriloquism effect. Temporally misaligned lights can also affect the latency of auditory responses. However, it remains unclear how multiple visual stimuli that differ from sounds in both space and time jointly influence localization behaviour. We investigated how visual distractors, spatially misaligned by 10{degrees}, presented before and/or during a target sound influence localization accuracy and response latency in a rapid head-pointing task. Human listeners localized brief (150 ms) broadband noise bursts with an average root-mean-square error of 5{degrees} and a baseline latency of 252 ms. Simultaneous visual cues induced the ventriloquism effect, in which the perceived sound location was biased by 1.8{degrees}. Response latency also increased by 21 ms (273 ms). Preceding visual stimuli (2 s duration) did not induce a bias, but increased latency by 55 ms (307 ms). Introducing a 200 ms gap between the preceding light and the sound reduced this latency increase to 24 ms (276 ms), still not inducing a significant bias. When we presented both a preceding and a simultaneous light on opposite sides of the sound, localization reflected the bias induced by the simultaneous light (1.8{degrees}) and the latency increase induced by the preceding light (by 48 ms). These findings reveal a dissociation in audiovisual integration: preceding visual stimuli primarily influence when a sound is responded to (latency), while simultaneous stimuli influence where it is perceived (accuracy). This supports causal inference models of multisensory integration and suggests distinct underlying mechanisms for spatial and temporal processing of sounds in sensorimotor circuits.
Linan Moyano, S.; Companys Oliva, B.; Alvarez Sanchez, A.; Turo Silanes, M.; Rodero, C.; Salvador Costa, X.; Piera, J.
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BioBlitzes are widely used citizen science events that combine biodiversity monitoring, public participation, and environmental awareness through short and intensive observation campaigns. However, applying this model to marine environments presents additional challenges related to safety, access, weather dependency, specialised equipment, species identification, and sustained participation. This paper presents the BioMARathon model as a case study of how BioBlitz-inspired events can be adapted to marine citizen science contexts. The BioMARathon extends the conventional BioBlitz format into a longer, seasonal, and distributed engagement model designed specifically for marine and coastal environments. The paper describes the conceptual foundations of the model in the Janus Engagement Framework, which informed both the design of the BioMARathon and the adaptation of the MINKA citizen science observatory to better support participation, validation, feedback, and continuity over time. BioMARato Catalunya, launched in 2021, is presented as the founding implementation of the model and as the basis for later replication in Portugal. Between 2021 and 2025, BioMARato Catalunya showed continued growth in participation, observations, and taxonomic coverage, while also contributing to the detection of non-indigenous species, first regional records, and climate-related ecological impacts. Beyond biodiversity outcomes, the case suggests that extending participation across a season, distributing activities through local mobilising organisations, and combining expert validation with visible feedback mechanisms can support recurrent participation, retention, and community reactivation in marine citizen science. Rather than offering a formal causal evaluation, this article contributes practical lessons for the design of citizen science initiatives in challenging environments.
Chimi, P. M.; Yonga, G.; Tchopwe Menkamla, A.; Maralossou, B.; Ngon Dikoume, A. M.; Mazak Nguihi, L.; Mvondo Effa, U. D.; Bell, J. M.; Mala, W. A.
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Climate-smart agriculture (CSA) dominates African agricultural policy discourse, yet fifteen years post-conceptualization, its transformative potential remains unrealized. Bibliometric analysis of 161 Scopus-indexed publications (2014-2025) reveals exponential field growth (31.3% annually) coupled with on technical dimensions and systemic neglect of financial mechanisms. Network analysis (VOSviewer), semantic mapping and citation bibliometrics expose cognitive oligopolisation--wherein 1.8% of authors generate 45% of output--geographical fragmentation into weakly connected regional clusters, and critical underrepresentation of the vulnerable Sahel. Despite 46.6% of publications addressing economic themes, merely 5.6% rigorously integrate financial analysis with adoption variables; terms including investment, cost-benefit and climate finance remain absent from major semantic clusters. The concept of structural financial ambiguity is introduced to characterize the maintenance of CSA in operational indeterminacy through academic discourse that substitutes description for actionable financial theorization. Paradigmatic transformation conditions are identified through emerging scholarship employing discrete choice experiments and cost-benefit evaluations to construct requisite knowledge foundations. Findings indicate that without comprehensive theorization of microfinance, digital finance, index-based insurance and payments for environmental services, international climate commitments risk implementation failure due to absence of scientifically validated financial instruments rather than technical solutions.
Nkera-Gutabara, C.; Olubayo, L. A. I.; Oduaran, O. H.; Kisiangani, I.; Khoza, S.; Gama, K.; Maritze, M.; Mabunda, C.; Keya, D.; Adetunji, K. E.; Tollman, S.; Micklesfield, L. K.; Mohamed, S. F.; Gomez-Olive, F. X.; Tluway, F.; Ramsay, M.; Bhatt, A. S.; Hazelhurst, S.; Maghini, D. G.; AWI-Gen Collaborative Centre, ; MADIVA Research Hub,
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Returning individualized microbiome results in ways that are ethical, comprehensible, and useful remains under-explored in African settings. We nested a multi-site, mixed-methods study within the AWI-Gen Wave 2 gut microbiome sub-study of 1,801 women aged 42 - 86 years to engage the participants and provide feedback. All (1,001) participants from Agincourt and Soweto (South Africa) and Nairobi (Kenya) were invited to feedback meetings: 496 from Agincourt, 87 from Soweto, and 195 from Nairobi responded. Engagement strategies were tailored by site (small-group and home-based sessions, visual metaphors, Foldscopes, and local-language delivery). Using semi-structured discussions and structured observations analysed thematically in MAXQDA under COREQ, five cross-cutting themes emerged: (1) understanding of microbiome reports, (2) emotional responses to feedback, (3) perceived health relevance, (4) trust in research institutions, and (5) suggestions for improving engagement. Culturally grounded explanations and local-language facilitation enhanced comprehension and perceived relevance; English-heavy sessions were associated with more confusion. Most participants expressed satisfaction and described planned or enacted dietary and lifestyle changes, while frustration centred on long delays between sampling and feedback. Trust increased with transparency and individualized return of results but was often conditional on minimizing burdensome procedures such as repeat blood sampling (phlebotomy) and ensuring timely feedback. Engagement was feasible and low-cost (approximately USD 29-59 per participant) with site-specific resource needs. Limitations included constrained generalizability beyond the three study sites. Returning individualized microbiome findings in community settings in Africa is acceptable, feasible, and can motivate health-promoting behaviours when delivered promptly and in culturally and linguistically appropriate ways. IMPORTANCEMicrobiome studies rarely return individualized results in low-resource settings due to concerns about appropriate feedback and associated costs. This gap risks eroding trust and diminishing research impact. In three African communities, tailored feedback on gut microbiome profiles was provided to 778 women. By documenting a costed, multi-site engagement model and the themes influencing acceptance and actionability, this work offers a practical framework for ethically returning complex -omics results at scale in underrepresented populations - advancing scientific equity and strengthening community trust in microbiome research.
Pulavan, N.; Nenninger, A.; Mbuli, J.; Poklembova, J.; Dimitriu, T.
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Plasmid conjugation is central to plasmid maintenance and spread among bacteria. Conjugation assays in liquid or on solid media are commonly used to quantify plasmid conjugation rates. Plasmids with short, rigid conjugative pili are thought to conjugate more efficiently on surfaces, whereas plasmids encoding long, flexible pili can conjugate efficiently in liquid medium. However, this pattern has not been tested systematically. Here, we perform standardised conjugation assays on a collection of 13 conjugative plasmids belonging to families that play a key role in AMR transmission and encode different conjugative pili types. We confirm that only the plasmids encoding long flexible pili conjugate efficiently in liquid. Furthermore, most transconjugants that arise from liquid assays involving plasmids with short, rigid pili can be attributed to transfer happening after the assay itself, on the surface of selective plates. This effect is amplified when using auxotrophic rather than antibiotic resistance markers, and impacts measures of transfer and defence efficiency. Finally, most of the tested plasmids with short pili had very high conjugation rates on surfaces, suggesting their transfer is mostly limited by physical constraints.
Cacheux, L.; Dutrillaux, B.; Gerbault-Seureau, M.; Nicolas, V.; Ponger, L.; Bed'Hom, B.; Escude, C.
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BackgroundAlpha satellites, a superfamily of AT-rich tandem repeats, are the primary DNA component of centromeres in Platyrrhini and Catarrhini. Analyses of the human genome suggest that centromeres behave like biological ridges, with new alpha satellite families expanding at the centromere core, splitting and displacing older ones towards the pericentromeres. The Cercopithecini tribe, which displays an unusual chromosomal evolution involving multiple chromosomal fissions and centromere formations, represents a promising model to enhance our understanding of alpha satellite DNA evolutionary history. We previously applied targeted sequencing to centromere DNA from two distant species drawn from the Cercopithecini terrestrial and arboreal lineages, and characterized six alpha satellite families exhibiting varying mean sequence identities. MethodsCombining classical and molecular cytogenetics, we mapped the chromosomal distribution of these alpha satellite families across 13 Cercopithecini, one Papionini, and one Colobinae species. A nuclear marker-based phylogeny provided an evolutionary framework for interpretation. ResultsOur phylogeny identifies the terrestrial and arboreal lineages, and a newly designated swamp clade. We observed significant interspecies variations in alpha satellite patterns, including differences in presence/absence and distinct chromosomal distribution patterns (centromeric, pericentromeric, or subtelomeric). Families previously described as heterogeneous (83-87% mean sequence identity) exhibit a centromeric position in the swamp lineage, which is characterized by conserved karyotypes. In contrast, these families show a pericentromeric distribution in the terrestrial and arboreal lineages, replaced at the centromere core by more homogeneous families (95-98% mean sequence identity). In the arboreal clade, which is characterized by highly fissioned karyotypes, putative evolutionary new centromeres show a unique co-occurrence of highly homogeneous and heterogeneous families. Conclusion & ImplicationsWe propose a comprehensive evolutionary scenario for alpha satellite DNA in Cercopithecini, where younger families arise at the centromere core, shift toward the pericentromeres as they age, and eventually face extinction. Our study suggests that alpha satellite DNA and chromosomes evolve in an interdependent manner, with satellite diversification and displacement occurring in parallel with chromosome fissions and centromere repositioning. This comparative cytogenomic approach provides both support for the human-based evolutionary model for alpha satellite DNA and novel temporal insights into its diversification dynamics. Beyond evolutionary genomics, our findings highlight the potential of alpha satellite DNA to complement systematic studies in deciphering complex primate evolutionary histories.
Reisenberger, E.; Schabus, M.; Florea, C.; Angerer, M.; Reimann-Ayiköz, M.; Preiss, J.; Roehm, D.; Heib, D. P. J.; Fazelnia, C.; Ameen, M. S.
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In humans, the first year of life is characterized by rapid developmental changes, including substantial brain maturation. As a result, neural responses to auditory stimuli undergo marked changes during this period. In this study, we followed 69 infants across their first year of life and recorded high-density electroencephalography (hdEEG) at 2 weeks, 6 months, and 12 months postpartum. Infants were presented with pure beep tones to examine the development of neural responses to auditory stimulation. We analysed event-related potentials (ERPs), inter-trial phase coherence (ITPC), and time-frequency (TF) responses to the beep tones and controlled for arousal state during stimulus presentation. We found that with increasing age, neural responses became more pronounced and showed reduced trial-to-trial variability. Phase synchronization increased from 2 weeks to later developmental stages in a broad low-frequency range (0 to 11 Hz), indicating improved temporal alignment of brain responses over time. However, phase synchronization decreased from 6 to 12 months, suggesting a developmental transition towards more differentiated brain activity. Taken together, these findings demonstrate that auditory maturation during the first year of life follows a non-linear trajectory driven by dynamic changes in neural synchronization, reflecting the progressive refinement of functional neural circuits. Our results thus provide a critical benchmark for understanding the neural dynamics underlying sensory development during this period. Impact StatementLongitudinal high-density EEG recordings reveal that neural responses to auditory stimuli undergo non-linear developmental changes during the first year of life, driven by dynamic shifts in neural synchronization that reflect progressive refinement of auditory neural processing.