Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton

Understanding the mechanisms that determine how phytoplankton adapt to warming will substantially improve the realism of models describing ecological and biogeochemical effects of climate change. Here, we quantify the evolution of elevated thermal tolerance in the phytoplankton, Chlorella vulgaris. Initially, population growth was limited at higher temperatures because respiration was more sensitive to temperature than photosynthesis meaning less carbon was available for growth. Tolerance to high temperature evolved after ≈ 100 generations via greater down-regulation of respiration relative to photosynthesis. By down-regulating respiration, phytoplankton overcame the metabolic constraint imposed by the greater temperature sensitivity of respiration and more efficiently allocated fixed carbon to growth. Rapid evolution of carbon-use efficiency provides a potentially general mechanism for thermal adaptation in phytoplankton and implies that evolutionary responses in phytoplankton will modify biogeochemical cycles and hence food web structure and function under warming. Models of climate futures that ignore adaptation would usefully be revisited

Scaling the effects of warming on metabolism from organisms to ecosystems

Understanding the impact of warming on organisms, communities and ecosystems is a central problem in ecology. Although species responses to warming are well documented, our ability to scale up to predict community and ecosystem properties is limited. Improving understanding of the mechanisms that link patterns and processes over multiple levels of organisation and across spatial and temporal scales promises to enhance our ability to predict whether the biosphere will exacerbate, or mitigate, climate warming. In this thesis, I combine ideas from metabolic theory with a variety of experimental approaches to further our understanding of how warming will impact photosynthesis and respiration across scales. Firstly, I show how phytoplankton can rapidly evolve increased thermal tolerance by downregulating rates of respiration more than photosynthesis. This increased carbon-use efficiency meant that evolved populations allocated more fixed carbon to growth. I then explore how constraints on individual physiology and community size structure influence phytoplankton community metabolism. Using metabolic theory, I link community primary production and respiration to the size- and temperature- dependence of individual physiology and the distribution of abundance and body size. Finally, I show that selection on photosynthetic traits within and across taxa dampens the effects of temperature on ecosystem-level gross primary production in a set of geothermal streams. Across the thermal-gradient, autotrophs from cold streams had higher photosynthetic rates than autotrophs from warm streams. At the ecosystem-level, the temperature-dependence of gross primary productivity was similar to that of organism-level photosynthesis. However, this was due to covariance between biomass and stream temperature; after accounting for the effects of biomass, gross primary productivity was independent of temperature. Collectively, this work emphasises the importance of ecological, evolutionary and physiological mechanisms that shape how metabolism responds to warming over multiple levels of organisation. Incorporating both the direct and indirect effects of warming on metabolism into predictions of the biosphere to climate futures should be considered a priority

MultiTurnCleanup: A Benchmark for Multi-Turn Spoken Conversational Transcript Cleanup

Current disfluency detection models focus on individual utterances each from a single speaker. However, numerous discontinuity phenomena in spoken conversational transcripts occur across multiple turns, hampering human readability and the performance of downstream NLP tasks. This study addresses these phenomena by proposing an innovative Multi-Turn Cleanup task for spoken conversational transcripts and collecting a new dataset, MultiTurnCleanup1. We design a data labeling schema to collect the high-quality dataset and provide extensive data analysis. Furthermore, we leverage two modeling approaches for experimental evaluation as benchmarks for future research.Comment: EMNLP 2023 main conference. Dataset: https://github.com/huashen218/MultiTurnCleanu

Associations between abundances of free-roaming gamebirds and common buzzards Buteo buteo are not driven by consumption of gamebirds in the buzzard breeding season

Releasing gamebirds in large numbers for sport shooting may directly or indirectly influence the abundance, distribution and population dynamics of native wildlife. The abundances of generalist predators have been positively associated with the abundance of gamebirds. These relationships have implications for prey populations, with the potential for indirect impacts of gamebird releases on wider biodiversity. To understand the basis of these associations, we investigated variation in territory size, prey provisioning to chicks, and breeding success of common buzzards Buteo buteo, and associations with variation in the abundances of free- roaming gamebirds, primarily pheasants Phasianus colchicus, and of rabbits Oryctolagus cuniculus and field voles Microtus agrestis, as important prey for buzzards. The relative abundance of game-birds, but not those of rabbits or voles, was weakly but positively correlated with our index of buzzard territory size. Gamebirds were rarely brought to the nest. Rabbits and voles, and not gamebirds, were provisioned to chicks in proportion to their relative abundance. The number of buzzard chicks increased with provisioning rates of rabbits, in terms of both provisioning frequency and biomass, but not with provisioning rates for gamebirds or voles. Associations between the abundances of buzzards and gamebirds may not be a consequence of the greater availability of gamebirds as prey during the buzzard breeding season. Instead, the association may arise either from habitat or predator management leading to higher densities of alternative prey (in this instance, rabbits), or from greater availability of gamebirds as prey or carrion during the autumn and winter shooting season. The interactions between gamebird releases and associated practices of predator control and shooting itself require better understanding to more effectively intervene in any one aspect of this complex social-ecological system

Parallel evolution of Pseudomonas aeruginosa phage resistance and virulence loss in response to phage treatment in vivo and in vitro

With rising antibiotic resistance, there has been increasing interest in treating pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. Negative effects of resistance may be mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolves to overcome resistance. Resistance evolution and its consequences are contingent on the bacteria-phage combination and their environmental context, making therapeutic outcomes hard to predict. One solution might be to conduct ‘in vitro evolutionary simulations’ using bacteria-phage combinations from the therapeutic context. Overall, our aim was to investigate parallels between in vitro experiments and in vivo dynamics in a human participant. Evolutionary dynamics were similar, with high levels of resistance evolving quickly with limited evidence of phage evolution. Resistant bacteria—evolved in vitro and in vivo—had lower virulence. In vivo, this was linked to lower growth rates of resistant isolates, whereas in vitro phage resistant isolates evolved greater biofilm production. Population sequencing suggests resistance resulted from selection on de novo mutations rather than sorting of existing variants. These results highlight the speed at which phage resistance can evolve in vivo, and how in vitro experiments may give useful insights for clinical evolutionary outcomes

Denial of long-term issues with agriculture on tropical peatlands will have devastating consequences

Non peer reviewe

Data from: Padfield et al. (2016) Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters.

<p>This repository provides the data from the TPC and logistic growth curves from the paper:</p> <p>Padfield, D., Yvon‐Durocher, G., Buckling, A., Jennings, S., & Yvon‐Durocher, G. (2016). Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters, 19(2), 133-142.</p> <p>metadata.pdf gives a more detailed explanation of the data.</p