Biology subjects

Beckerman, A.

Publications and source records attributed to Beckerman, A..

6 recordsLinked to original sources

bioRxiv2025

Intracellular niche specialisation drives evolutionary entrapment of endosymbiotic algae

Endosymbiosis underpins the evolution of complex life and the function of diverse ecosystems, but the mechanisms driving the origin and stability of endosymbiosis remain unclear. Fitness trade-offs between intracellular and extracellular niches could drive the emergence of stable endosymbiosis if adaptation to the intracellular niche reduces fitness in the extracellular niche, reinforcing endosymbiosis through niche specialisation by the endosymbiont. We tested this hypothesis by quantifying phenotypic divergence between endosymbiotic and free-living populations of a facultative algal endosymbiont along trait axes predicted to contrast between its intracellular and extracellular lifestyles. Consistent with endosymbiont specialisation, we observed strong divergence involving multiple traits between endosymbiotic and free-living populations. Specifically, endosymbionts showed convergent losses of multiple nitrogen metabolism pathways, increased export of maltose and glucose, increased sensitivity to acidification, higher and less variable photosynthetic efficiency, and reduced free-living growth rate. Intracellular environments are stable, safe from natural enemies, and come with a reliable supply of specific nutrients, but are acidic and place demands upon endosymbionts to provision their hosts; our data suggest that adapting to this niche is likely to reduce free-living growth and survival of endosymbionts. Our findings support fitness trade-offs between contrasting intracellular and extracellular environments as a mechanism stabilising endosymbiosis by driving evolutionary entrapment of niche-specialist endosymbionts.

evolutionary biology↗

bioRxiv2023

Nest site selection and productivity of a critically endangered parrot, the great green macaw (Ara ambiguus) in an anthropogenic landscape

Nest site selection is the principal way secondary cavity-nesting species mitigate the negative effects of factors such as predation, parasitism and exposure on productivity. High-quality cavities could then be expected to be selected in response to the primary threat to nest success. Understanding how demographic rates are affected by anthropogenic changes to ecosystems is vital if effective conservation management strategies are to be developed and implemented. Large-bodied secondary cavity-nesting birds rely on large cavities in mature trees that are often absent or reduced in anthropogenically disturbed forests. Thus, the availability of high-quality nest sites may be limited for these species, potentially reducing productivity. The aim of this study was to investigate nest-site selection and the effect of nest-site features on productivity in the critically endangered great green macaw (Ara ambiguus) in northern Costa Rica. We show that great green macaws select nest sites according to the characteristics of the cavity and of the tree in which they are located. Moreover, productivity was a function of certain cavity features. We conclude that great green macaws are not reliant on primary forest for nest sites and typically choose cavities in remnant, isolated trees in pasture or young secondary forests.

ecology↗

bioRxiv2022

Using passive acoustic monitoring to estimate the abundance of wide-ranging species in tropical rainforest ecosystems

Most conservation relies on being able to estimate population size accurately. The development, implementation and adaptation of effective conservation strategies rely on quantifying the impacts of different threats on population dynamics, identifying species that need conservation management, and providing feedback on the effectiveness of any management actions. However, current approaches are not suitable for wide-ranging species that reside in tropical ecosystems. Here we use the great green macaw Ara ambiguus as a case study to show that passive acoustic monitoring is an effective tool for collecting data that can then estimate abundance. We estimate a population of 485.65 {+/-} 61 SE great green macaws in Costa Rica during the breeding, suggesting the population here is larger than previously estimated. We have also highlighted potentially important areas for the species in regions that had not previously been studied. We have demonstrated at a population scale that passive acoustic monitoring (PAM) offers conservationists an efficient and effective way to understand population dynamics. With a high proportion of parrot species threatened globally, passive acoustic monitoring will enable effective monitoring and become an essential tool in conservation planning and evaluation. PAM technology has enormous potential to facilitate such assessments because it is easily scalable, recordings can be stored and re-analysed as machine learning, and abundance estimation techniques become more advanced.

ecology↗

bioRxiv2022

Inadequate sampling of the soundscape leads to overoptimistic estimates of recogniser performance: a case study of two sympatric macaw species

Passive acoustic monitoring (PAM) - the use of autonomous recording units to record ambient sound - offers the potential to dramatically increase the scale and robustness of species monitoring in rainforest ecosystems. PAM generates large volumes of data that require automated methods of target species detection. Species-specific recognisers, which often use supervised machine learning, can achieve this goal. However, they require a large training dataset of both target and non-target signals, which is time-consuming and challenging to create. Unfortunately, very little information about creating training datasets for supervised machine learning recognisers is available, especially for tropical ecosystems. Here we show an iterative approach to creating a training dataset that improved recogniser precision from 0.12 to 0.55. By sampling background noise using an initial small recogniser, we can address one of the significant challenges of training dataset creation in acoustically diverse environments. Our work demonstrates that recognisers will likely fail in real-world settings unless the training dataset size is large enough and sufficiently representative of the ambient soundscape. We outline a simple workflow that can provide users with an accessible way to create a species-specific PAM recogniser that addresses these issues for tropical rainforest environments. Our work provides important lessons for PAM practitioners wanting to develop species-specific recognisers for acoustically diverse ecosystems.

ecology↗

bioRxiv2021

Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex

Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. To address this basic question, we studied the ecological and evolutionary dynamics of polymorphism in reproductive strategy in a metapopulation of the model facultative sexual, Daphnia pulex, located in the southern United Kingdom. We found that patterns of clonal diversity, but not genetic diversity varied with ephemerality. Reconstruction of a multi-year pedigree demonstrated the co-existence of clones that were found to differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative QTL underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.

evolutionary biology↗

bioRxiv2019

Designing synthetic bacterial consortia for landfill leachate treatment based on community matrices and regression tree analysis

The performance of microbial communities exploited by industry are largely optimised by manipulating process parameters, such as flow rates, growth conditions, and reactor parameters. Conversely, the composition of microorganisms used are often viewed as a "black box". This is mostly due to the relatively high costs and technical expertise required to identify and quantify the microbial consortia, as well as limited tools to create functional assemblages. Unknown details about the interactions among species may impose a limit on how much microbial function can be optimised for industrial purposes. Here, a new workflow was developed for studying microbial consortia using high throughput, species and community specific measurements of growth rates and yields. Growth rate and yield among all single, pairwise, triple, quadruples, quintuple and sextuple combinations of six bacterial isolates on landfill leachate were evaluated. Additive, antagonistic (e.g. competitive) or synergistic (+/-) interactions can be inferred from the rate and yield data. We found that antagonistic interactions, which hinder growth and yield, were the dominant interaction type, with only a few synergistic interactions observed. Mixed effects models were used to investigate the relationship between interaction type and species richness (biodiversity). Community identity was found to be a more important factor in predicting yield determining interactions but not rate determining interactions. Species richness was a good predictor of rate determining interactions, with the most positive interactions happening at a low species richness. Regression tree analysis identified Lysinibacillus sp. as a keystone species, a genus previously associated with bioremediation. Its presence led to a drastic change in the function of the synthetic ecosystem, with both positive yield and rate determining interactions. We were able to infer interactions about specific pairs of species, and the competitive/synergistic tendencies of single species from only basic top-down growth measurements. In this way, we have demonstrated how factorial experiments using isolated microorganisms can be used to ultimately design synthetic consortia with desirable traits for industry. Funding statementThis research was funded by the EPSRC (Vacation Bursary Award), BBSRC (Impact Acceleration Award), Department of Chemical and Biological Engineering, The University of Sheffield (Summer Undergraduate Research Fellowship) and Viridor Ltd. Ethics statements(Authors are required to state the ethical considerations of their study in the manuscript, including for cases where the study was exempt from ethical approval procedures) Does the study presented in the manuscript involve human or animal subjects: No Data availability statementGenerated Statement: This manuscript contains previously unpublished data. The name of the repository and accession number are not available.

microbiology↗