Philosophical Transactions of the Royal Society B

1.Plastic traits, capable of taking multiple forms, often correlate with one another or with features of the environment when measured over time. These patterns of correlated change are sometimes assumed to reflect adaptive plasticity, such as coevolved "integrated phenotypes" within individuals, synchronisation between social or mating partners, or responses to environmental gradients. 2. Such plasticity is ecologically and evolutionarily important, so there is considerable interest in understanding how it varies between individuals and groups. However, "regression to the mean", the statistical tendency for traits to revert to the average value, may create the illusion of strong bivariate correlations in timeseries data, including substantial but meaningless variation between individuals. 3. We demonstrate this using simulated and real data, revealing how regression to the mean can create bias both within and between samples. We then show, however, that its effects can often be eliminated using autoregressive models. 4. We also offer a detailed discussion of how and why regression to the mean arises, introducing the idea that it is both a statistical and ecological phenomenon.

Both vocalization and gesture are universal modes of communication and fundamental features of language development. Many believe that language evolved out of early gestural use; however, evidence reported here suggests vocalization precedes gesture in human communication and forms the predominant foundation for language. To our knowledge no prior research has investigated the rates of emergence of both gesture and vocalization in human infants to evaluate this question. We evaluated the rates of gesture and speech-like vocalizations (protophones) of 10 infants at 4, 7, and 11 months of age using parent-infant laboratory recordings. We found that infant protophones outnumbered gestures substantially at all three ages, ranging from >30 times more protophones than gestures at 3 months, to more than twice as many protophones as gestures at 11 months. The results suggest that vocalization is the predominant mode of communication in human infants from the beginning of life.

Within species, vocal and auditory systems co-evolve to converge on a critical temporal acoustic structure that can be best produced and perceived. While dogs cannot produce articulated sounds, they respond to speech, raising the question as to whether this heterospecific receptive ability is shaped by exposure to speech or bounded by their own sensorimotor capacity. Acoustic analyses of vocalisations show that dogs main production rhythm is slower than the dominant (syllabic) speech rate, and that human dog-directed speech falls halfway in between. Comparative exploration of neural (electroencephalography) and behavioural responses to speech reveals that comprehension in dogs relies on a slower speech rhythm tracking (delta) than humans (theta), even though dogs are equally sensitive to human speech content and prosody. Thus, the dog audio-motor tuning differs from humans, who vocally adjust their speech rate to this shared temporal channel.

New scientific discoveries are communicated through multiple channels. Publications remain essential for scientists, whereas general public relies on news articles. Numerous studies investigated the path from publications to news and identified press releases as the key factor, associating them with issues such as exaggerations, but less is known about the direct influence of press releases on subject choice or on the content of media reports. Here, a cross-sectional sample of publications related to genetics and CRISPR is assessed in three independent datasets (n = 1362 publications, n = 461 press releases). Analysis finds 92.5% (CI = 88.5-96.5) dependence of news outlets on press releases in terms of topic choice and 39-43% explicit use of passages from press releases. Publications without press releases are described by 74x fewer news outlets. Even if they come from leading journals or universities, lack of a press release leads to 8.8x less coverage. Given the high impact of press releases, their reliability is especially relevant, but the majority of them omits interest disclosures - 84.3% (CI = 80.8-87.7) of press releases did not mention existing conflicts of interest, including multiple patent applications. These results establish the major indirect and direct role of press releases in science communication via online media. In line with previous research, this dependency raises concerns about possible distortions of science coverage.

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.

BackgroundA remarkable sequence in phage T4 causes ribosomes to skip over a 50 nucleotide insert within a topoisomerase subunit gene, and resume correct synthesis of the protein at a high efficiency. Its mechanism has been extensively studied but it remained an isolated phenomenon whose origin and full function are still a mystery. ResultsWe have found dozens of homologous cases in genomic and metagenomic sequences, all part of a mobile DNA element that repeatedly inserts in topoisomerase genes of Myoviridae phages. These have substantial sequence diversity, with selective conservation that specify the elaborate set of mechanisms found experimentally to underlie this extreme case of translational recoding. These sequences provide new variations on these mechanisms, and introduce additional features that may also be important for bypassing. These include a series of RNA secondary structures, a conserved stop codon or rare hungry codon at the start of the bypass, a Shine-Dalgarno sequence flanked by AU-rich sequence, and residues in the nascent peptide that prime the ribosome for bypassing. ConclusionsThese data provide an evolutionary foundation for the experimentally derived mechanisms, highlight several new features of the sequence, and provide substantial new variations on the bypass theme that will allow further experimental exploration of biologically meaningful variants.

Geographic differences in vocalisations provide strong evidence for animal culture, with patterns likely arising from generations of social learning and transmission. The current knowledge on the evolution of vocal variation has predominantly focused on fixed repertoire, territorial song in passerine birds. The study of vocal communication in open-ended learners and in contexts where vocalisations serve other functions is therefore necessary for a more comprehensive understanding of vocal dialect evolution. Parrots are open-ended vocal production learners that use vocalisations for social contact and coordination. Geographic variation in parrot vocalisations typically take the form of either distinct regional variations known as dialects or graded variation based on geographic distance known as clinal variation. In this study, we recorded monk parakeets (Myiopsitta monachus) across multiple spatial scales (i.e. parks and cities) in their European invasive range. We then compared calls using a multi-level Bayesian model and sensitivity analysis, with this novel approach allowing us to explicitly compare vocalisations at multiple spatial scales. We found support for founder effects and/or cultural drift at the city level, consistent with passive cultural processes leading to large scale dialect differences. We did not find a strong signal for dialect or clinal differences between parks within cities, suggesting that birds did not actively converge on a group level signal, as expected under the group membership hypothesis. We demonstrate the robustness of our findings and offer an explanation that unifies the results of prior monk parakeet vocalisation studies.

Understanding how opposing regulatory factors shape gene expression is essential for interpreting complex biological systems. A motivating observation, drawn from cancer epigenetics, is that removing an activating factor can sometimes lead to higher, not lower, expression of a gene that is also subject to repression. This counterintuitive behavior suggests that competition between activators and repressors for limited genomic binding sites may produce unexpected transcriptional outcomes. Prior theoretical work proposed this mechanism, but it has been difficult to test directly in natural systems, where layers of chromatin regulation obscure causal relationships. This paper introduces a fully synthetic, tunable genetic platform in a prokaryotic model system that isolates this competition mechanism in a clean and interpretable setting. The engineered construct contains a target gene with binding sites for both an activator and a repressor, together with a separate decoy region that carries overlapping binding sites for the same regulators. Activator and repressor functions are implemented using CRISPRa and CRISPRi, which permit independent control of regulator expression levels and binding affinities. Using this minimal system, the paper shows that increasing activator expression can reduce expression of the target gene when both regulators are present, consistent with the prediction that additional activator molecules displace the repressor from decoy sites and allow it to more effectively repress the target. By demonstrating how competition alone can invert expected regulatory responses, this synthetic framework provides a validated model for understanding similar paradoxical behaviors in natural regulatory networks and establishes a foundation for future studies in more complex mammalian contexts.

While biodiversity decline continues and laypeoples knowledge about species is limited, especially in children, high-quality communication is needed to raise awareness. For this, communicators should be aware of current knowledge levels in their target groups. We compared biodiversity communicators' estimates of the average species literacy level in primary school children with the actual level. Moreover, we explored the importance that communicators placed on species literacy and the level that they desired. Estimations of childrens average knowledge level varied widely and differed from the actual level. In particular, communicators overestimated the species literacy level. Although most biodiversity communicators agreed that knowledge about species is important, their view differed as to why species literacy would be important. Moreover, communicators differed with respect to the relative importance attached to different knowledge components. Professionals may thus benefit from a detailed framework of species literacy that illustrates different aspects and values. Most importantly, our findings suggest that to bridge the gap between actual and desired knowledge levels in children effectively, biodiversity communicators first need to become more aware of current perceptions in young audiences.

Translational processes that facilitate effective interdisciplinary communication remain a black box. Here, we aimed to operationalize translational practices by combining conversation analysis and network science to analyze interdisciplinary research meetings. We applied conversation analysis to transcribed meetings, and identified chair, clarifying, skeptical, expert, connecting, and practical actions. For each meeting, we constructed a network ( meetome) with team members as nodes, and the number of consecutive speaking turns between members as links. We found that the relative occurrence of role-specific actions correlated with network measures. We discuss how awareness of interactional roles within meetings may help to implement a translational approach in interdisciplinary research teams.

Science communication (sci-comm) encompasses activities that promote scientific literacy, inform policy, and inspire future scientists. Despite its value, sci-comm is often considered less pretigious than research and other internal academic activities. In Australia, scientific organisations (e.g., learned societies) rely on members to perform a range of sci-comm activities, typically unpaid. In this pilot study, we surveyed 88 Australian life sciences organisations to examine who performs sci-comm and why. Most respondents were early-career women employed in university research positions. Participants largely agreed that organisational sci-comm brought limited career benefits and was often viewed as feminised or "care work" relative to their research roles. Yet, respondents also cited personal and professional gains and most wished to continue in such roles. Our findings suggest "invisible" sci-comm performed for scientific organisations is disproportionately undertaken by women at early career stages, with implications for career progression and gender equity in STEM.

We examine every Inclusive Teaching section in articles published by the journal CourseSource - undergraduate biology teaching materials and related essays - from 2014 to 2022 to understand the evolution of inclusive teaching ideas as expressed through language. We find a rapid shift in attention to inclusive teaching occurs between 2018 and 2019, marked by an increase in section length, increased use of inclusive teaching keywords, and an increase in complexity of ideas in the semantic network. This critical transition occurs before many of the recent events in 2020 which have renewed conversation on equity in education. Some effect is associated with Writing Workshop Faculty Mentoring Networks, which provide participants with authoring resources and support. However, this alone is not enough to explain the observed shift, suggesting that many other structures, conversations, and investments were already providing the fertile ground for educational equity in biology education.

Due to the important role they play in the antimicrobial resistance (AMR) crisis and in microbial evolution in general, a great deal of empirical and theoretical work is currently underway, trying to understand plasmid ecology. One of the key questions is how these often costly genetic elements persist in host populations. Here I show that when modelling plasmid population dynamics, it is not sufficient to treat them as always costly (or beneficial). I argue that conjugation related costs may be more important to plasmids in nature than they are in benign laboratory settings. Furthermore, I show that these conjugation related costs can be very severe and still not lead to extinction of a plasmid from a host population.

This integrative literature review analyzes the corpus of biology education research published in the main biology education journals of major professional societies. The goal of this analysis is to determine which approaches (including groups of focus, research methods, and settings/perspectives) from social science fields (i.e., psychology, sociology, and anthropology) are utilized in published peer-reviewed biology education research relating to diversity, equity and inclusion (DEI). Scoping how social science approaches are used in this area is important to understanding whether biology education research could benefit from complementary approaches that might advance praxis. This analysis found that research informing the biology education community draws heavily from psychological perspectives that are overwhelmingly not disaggregated (78% of articles identifying a group used a lumped together one), are by far more quantitative (58% used survey, 26% grades, 20% school data) than qualitative (17% used interview, 10% observation), and did not (72%) adopt structural approaches. The addition of missing contributions from social science is critical to advancing interventions to broaden STEM participation given that merging paradigms can offer more robust, multi-level explanations for observed phenomena. This has important implications for education, biology education, biology education research, social science, and research in related STEM fields.

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.

Gender inequality has been documented across a variety of high-prestige professions. Both structural bias (e.g., lack of proportionate representation) and interpersonal bias (e.g., sexism, discrimination) generate costs to underrepresented minorities. How can we estimate these costs and what interventions are most effective for reducing them? We used agent-based simulations, removing gender differences in interpersonal bias to isolate and quantify the impact and costs of structural bias (unequal gender ratios) on individuals and institutions. We compared the long-term impact of bias-confrontation strategies. Unequal gender ratios led to higher costs for female agents and institutions and increased sexism among male agents. Confronting interpersonal bias by targets and allies attenuated the impact of structural bias. However, bias persisted even after a structural intervention to suddenly make previously unequal institutions equal (50% women) unless the probability of interpersonal bias-confrontation was further increased among targets and allies. This computational approach allows for comparison of various policies to attenuate structural equality, and informs the design of new experiments to estimate parameters for more accurate predictions.

While scientific environments have been described as unwelcoming to the LGBTQ+ community, and fields such as physics have systematically documented these challenges, the climate in biology workplaces has not been assessed. We conducted the largest survey to date of LGBTQ+ biologists to examine how their sense of belonging and perception of climate in the biology workplace and professional societies compare to that of their straight and cis peers. We surveyed 1419 biologists across five professional societies, with 486 identifying as LGBTQ+. Trans and gender non-conforming (TGNC) biologists reported lower belonging and morale within the workplace, professional societies, and the biology community compared to cis, straight biologists. They also reported being less comfortable with the climate of various professional biology environments. While LGBTQ+ biologists report that their workplaces are moderately inclusive, over 20% of all LGBTQ+ biologists and nearly 40% of TGNC biologists experience exclusionary behavior at work. This landmark survey provides the first comprehensive analysis of the LGBTQ+ climate in biology, revealing specific challenges faced by TGNC scientists and identifying interventions to enhance inclusivity for scientists. Significance StatementThis landmark study includes the largest known sample of LGBTQ+ biologists and offers the first comprehensive description of the LGBTQ+ climate in biology, differentiating between the experiences of cisgender lesbian, gay, bisexual, and queer (LGBQ) biologists and transgender and gender non-conforming (TGNC) biologists. The study found that compared to non-LGBTQ+ biologists, TGNC participants report lower belonging, morale and comfort with the climate across biology workplaces, professional societies, and the biology community. While on average LGBTQ+ participants reported that their workplaces are moderately inclusive, over 20% of all LGBTQ+ biologists and nearly 40% of TGNC biologists report experiencing exclusionary behaviors at work. The study offers immediate implications for institutional policies and professional development in the biological sciences.

Effective communication in birds is often hampered by background noise, with many recent studies focusing on the effect of anthropogenic noise on passerine bird song. Continuous low-frequency natural noise is predicted to drive changes in both frequency and temporal patterning of bird vocalizations, but the extent to which these effects may also affect birds that lack vocal learning is not yet fully understood. Here we use a gradient of exposure to natural low-frequency noise to assess whether it exerts selective pressure on vocalizations in a species whose songs are innate. We tested whether three species of Pogoniulus tinkerbirds adapt their song when exposed to a source of continuous low-frequency noise from ocean surf. We show that dominant frequency increases the closer birds are to the coast in all the three species, and in line with higher noise levels, indicating that ocean surf sound may apply a selective pressure on tinkerbird songs. As a consequence, tinkerbirds adapt their songs with an increase in frequency to avoid the masking effect due to overlapping frequencies with ambient noise, therefore improving long-range communication with intended receivers. Our study provides for the first time, compelling evidence that natural ambient noise affects vocalizations in birds whose songs are developed innately. We believe that our results can also be extrapolated in the context of anthropogenic noise pollution, hence providing a baseline for the study of the effects of low-frequency ambient noise on birds that lack vocal learning. Significance StatementBirdsong is constantly under selection as it mediates key interactions such as mate attraction, competition with same-sex individuals for reproduction and competition with heterospecifics for space-related resources. Any phenomenon that interferes with communication can therefore have a profound impact on individual fitness. Passerines are more likely to avoid the masking effect of background noise because of their higher vocal flexibility. Many non-passerine species lacking such flexibility might therefore be more vulnerable to the negative effects on their fitness of exposure to low-frequency background noise. Species incapable of adapting their signals to background noise are predicted to disappear from noisy areas. Despite this, we show that species that lack song learning may show an adaptive response to natural noise which may develop over evolutionary timescales.

Evolution by natural selection is recognized as both the most important concept in undergraduate biology and the most difficult to teach. Unfortunately, teaching and assessment of evolution have been impaired by legacy approaches that focus on Darwins original insights and the Modern Synthesis integration of Mendelian genetics, but ignore or downplay advances from what we term the Molecular Synthesis. To create better alignment between instructional approaches and contemporary research in the biosciences, we propose that the primary learning goal in teaching evolution should be for students to connect genotypes, phenotypes, and fitness. To support this approach, we developed and tested assessment questions and scoring rubrics called the Extended Assessing Conceptual Reasoning of Natural Selection (E-ACORNS) instrument. Initial E-ACORNS data suggest that after traditional instruction, few students recognize the molecular synthesis--prompting us to propose that introductory course sequences be re-organized with the molecular synthesis as their central theme.

Mutualistic ecological networks can suddenly transition to undesirable states, due to small changes in environmental conditions. Recovering from such a collapse can be difficult as reversing the original environmental conditions may be infeasible. Additionally, such networks can also exhibit hysteresis, implying that ecological networks may not recover. Here, using a dynamical eco-evolutionary framework, we try to resurrect mutualistic networks from an undesirable low-functional collapse state to a high-functioning state. We found that restoring the original environmental conditions rarely aided in recovering the original network due to the presence of hysteresis. By combining concepts from signal propagation theory and eco-evolutionary dynamical modeling, we show that network resurrection could be readily achieved by perturbing a single species that controls the response of the dynamical networks. We show that during the resurrection of collapsed networks, the historical network architecture, levels of trait variation, and eco-evolutionary dynamics could aid in the revival of the network even in undesirable environmental conditions. Our study argues that focus should be applied to a few species whose dynamics one could steer to resurrect the entire network from a collapsed state.