Journal: Philosophical Transactions of the Royal Society B: Biological Sciences

Abbreviation

Phil. Trans. R. Soc. B

Publisher

Royal Society

Journal Volumes

ISSN

1471-2970
0962-8436

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Publications 1 - 10 of 85
  • The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations
    Item type: Journal Article
    Rieseberg, Loren H.; Widmer, Alex; Arntz, A. Michele; et al. (2003)
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • Preface
    Item type: Other Journal Item
    Rafajlović, Marina; Alexander, Jake; Butlin, Roger K.; et al. (2022)
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • The importance of regeneration processes on forest biodiversity in old-growth forests in the Pacific Northwest
    Item type: Journal Article
    Luu, Hoang; Hille Ris Lambers, Janneke; Lutz, James A.; et al. (2024)
    Philosophical Transactions of the Royal Society B: Biological Sciences
    Forest diversity is the outcome of multiple species-specific processes and tolerances, from regeneration, growth, competition and mortality of trees. Predicting diversity thus requires a comprehensive understanding of those processes. Regeneration processes have traditionally been overlooked, due to high stochasticity and assumptions that recruitment is not limiting for forests. Thus, we investigated the importance of seed production and seedling survival on forest diversity in the Pacific Northwest (PNW) using a forest gap model (ForClim). Equations for regeneration processes were fit to empirical data and added into the model, followed by simulations where regeneration processes and parameter values varied. Adding regeneration processes into ForClim improved the simulation of species composition, compared to Forest Inventory Analysis data. We also found that seed production was not as important as seedling survival, and the time it took for seedlings to grow into saplings was a critical recruitment parameter for accurately capturing tree species diversity in PNW forest stands. However, our simulations considered historical climate only. Due to the sensitivity of seed production and seedling survival to weather, future climate change may alter seed production or seedling survival and future climate change simulations should include these regeneration processes to predict future forest dynamics in the PNW. This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
  • The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies
    Item type: Journal Article
    Huisman, Jana; Vaughan, Timothy G.; Egli, Adrian; et al. (2022)
    Philosophical Transactions of the Royal Society B: Biological Sciences
    The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples are rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty of extracting plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find that chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long reads during assembly graph generation (Canu). By contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
  • The meaning of functional trait composition of food webs for ecosystem functioning
    Item type: Journal Article
    Gravel, Dominique; Albouy, Camille; Thuiller, Wilfried (2016)
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • Biological control and sustainable food production
    Item type: Journal Article
    Bale, J. S.; Lenteren, J.C. van; Bigler, F. (2008)
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • Effects of species interactions on the potential for evolution at species' range limits
    Item type: Journal Article
    Alexander, Jake; Atwater, Daniel Z.; Colautti, Robert I.; et al. (2022)
    Philosophical Transactions of the Royal Society B: Biological Sciences
    Species’ ranges are limited by both ecological and evolutionary constraints. While there is a growing appreciation that ecological constraints include interactions among species, like competition, we know relatively little about how interactions contribute to evolutionary constraints at species' niche and range limits. Building on concepts from community ecology and evolutionary biology, we review how biotic interactions can influence adaptation at range limits by impeding the demographic conditions that facilitate evolution (which we term a ‘demographic pathway to adaptation’), and/or by imposing evolutionary trade-offs with the abiotic environment (a ‘trade-offs pathway’). While theory for the former is well-developed, theory for the trade-offs pathway is not, and empirical evidence is scarce for both. Therefore, we develop a model to illustrate how fitness trade-offs along biotic and abiotic gradients could affect the potential for range expansion and niche evolution following ecological release. The model shows that which genotypes are favoured at species' range edges can depend strongly on the biotic context and the nature of fitness trade-offs. Experiments that characterize trade-offs and properly account for biotic context are needed to predict which species will expand their niche or range in response to environmental change.
  • Maximum Entropy Production allows a simple representation of heterogeneity in semiarid ecosystems
    Item type: Journal Article
    Schymanski, Stan; Kleidon, Axel; Stieglitz, Marc; et al. (2010)
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • Physiological response of Swiss ecosystems to 2018 drought across plant types and elevation
    Item type: Journal Article
    Gharun, Mana; Hörtnagl, Lukas; Paul-Limoges, Eugénie; et al. (2020)
    Philosophical Transactions of the Royal Society B: Biological Sciences
    Using five eddy covariance flux sites (two forests and three grasslands), we investigated ecosystem physiological responses to the 2018 drought across elevational gradients in Switzerland. Flux measurements showed that at lower elevation sites (below 1000 m.a.s.l.; grassland and mixed forest) annual ecosystem productivity (GPP) declined by approximately 20% compared to the previous 2 years (2016 and 2017), which led to a reduced annual net ecosystem productivity (NEP). At the high elevation sites, however, GPP increased by approximately 14% and as a result NEP increased in the alpine and montane grasslands, but not in the subalpine coniferous forest. There, increased ecosystem respiration led to a reduced annual NEP, despite increased GPP and lengthening of the growing period. Among all ecosystems, the coniferous forest showed the most pronounced negative stomatal response to atmospheric dryness (i.e. vapour pressure deficit, VPD) that resulted in a decline in surface conductance and an increased water-use efficiency during drought. While increased temperature enhanced the water-use efficiency of both forests, de-coupling of GPP from evapotranspiration at the low-elevation grassland site negatively affected water-use efficiency due to non-stomatal reductions in photosynthesis. Our results show that hot droughts (such as in 2018) lead to different responses across plants types, and thus ecosystems. Particularly grasslands at lower elevations are the most vulnerable ecosystems to negative impacts of future drought in Switzerland. This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
  • Insect antimicrobial peptides act synergistically to inhibit a trypanosome parasite
    Item type: Journal Article
    Marxer, Monika; Vollenweider, Vera; Schmid-Hempel, Paul (2016)
    Philosophical Transactions of the Royal Society B: Biological Sciences
Publications 1 - 10 of 85