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  • Journal article
    Tajadura-Ortega V, Chai W, Roberts LA, Zhang Y, Maio AD, Decout AC, Pinheiro BA, Palma AS, Nicola GD, Riaposova L, Gimeno-Molina B, Lee YS, Cao H, Piskarev V, Akune Y, Costa TRD, Amin H, Sykes L, Bennett PR, Marchesi JR, Feizi T, Liu Y, MacIntyre Det al., 2025,

    Identification and characterisation of vaginal bacteria-glycan interactions implicated in reproductive tract health and pregnancy outcomes

    , Nature Communications, Vol: 16, ISSN: 2041-1723

    Lactobacillus displacement from the vaginal microbiome associates with adverse health outcomes and is linked to increased risk of preterm birth. Glycans mediate bacterial adhesion events involved in colonisation and infection. Using customised glycan microarrays, we establish glycan interaction profiles of vaginal bacteria implicated in reproductive health. Glycan binding signatures of the opportunistic pathogens Escherichia coli, Fusobacterium nucleatum and Streptococcus agalactiae to oligomannose N-glycans, galactose-terminating glycans and hyaluronic acid, respectively are highly distinct from Lactobacillus commensals. Binding to sulphated glycosaminoglycans by vaginal bacteria is pH dependent, as is binding to neutral and sialic acid-terminating glycans by F. nucleatum. Adhesion of Lactobacillus crispatus, Lactobacillus iners, Gardnerella vaginalis, S. agalactiae and F. nucleatum to vaginal epithelial cells is partially mediated by chondroitin sulphate. S. agalactiae binding to chondroitin sulphate C oligosaccharides is inhibited by L. crispatus. This study highlights glycans as mediators of vaginal bacterial binding events involved in reproductive health and disease.
  • Journal article
    Alexandre YO, Potemkin N, Schienstock D, Duchamp B, Poch A, Christo SN, Li S, Qin L, Beattie L, Utzschneider DT, Ono M, Schroder J, Mackay LK, Mueller SNet al., 2025,

    Splenic fibroblastic reticular cells orchestrate dendritic cell maturation and facilitate CD8<SUP>+</SUP> T cell priming and protective memory

    , SCIENCE ADVANCES, Vol: 11
  • Journal article
    Bonnin RA, Jacquemin A, Pizzato J, Girlich D, Emeraud C, Kostrzewa M, Naas T, Larrouy-Maumus G, Dortet Let al., 2025,

    MALDI-TOF lipidomics rapidly detects modification of 2-hydroxymyristate lipid A, a potential virulence trait in <i>Enterobacter bugandensis</i>

    , MICROBIOLOGY SPECTRUM, Vol: 13
  • Journal article
    Schulte to Bühne H, Tobias JA, Durant SM, Pettorelli Net al., 2025,

    Land use configuration shapes climate change vulnerability of gallery forests in a savannah ecosystem

    , Global Ecology and Conservation, Vol: 59, ISSN: 2351-9894

    Interactions between anthropogenic pressures make it difficult to predict biodiversity change and plan conservation interventions. Climate change is expected to drive widespread ecological change in the tropics over the coming decades, but it is unclear where and when these changes are going to intensify, or reduce, the impacts of additional pressures from human land use. To address this uncertainty, we apply a novel vulnerability assessment framework to show how land use configuration modifies the extent of potential harms arising from climate change to gallery forests, an important vegetation type in tropical savannahs. We highlight how the spatial distribution of climate change (specifically, change in annual rainfall) interacts with the spatial distribution of land use (specifically, cropland), as well as the biophysical context of the study site (the W-Arly-Pendjari transboundary protected area in West Africa), to shape the vulnerability of gallery forests to changes in rainfall in the region. Due to the pathways by which rainfall change and land use interact, vulnerability is especially elevated in core protected areas, warranting particular attention from conservation managers. Overall, our work illustrates how unexpected patterns in potential negative consequences can arise through interactions between pressures on biodiversity, highlighting the importance of considering mechanistic pathways for predicting biodiversity outcomes under multifaceted global environmental change.
  • Journal article
    Salis A, Molina A, Mephane-Montel L, Chaine A, Schlenker P, Chemla Eet al., 2025,

    No effect of note order on the response of coal tits to conspecific, heterospecific and artificial mobbing calls

    , Ethology, Vol: 131, ISSN: 0179-1613

    Most Parid species produce specific, order-constrained mobbing calls. These calls elicit responses from both conspecifics and heterospecifics, with evidence indicating that such responses occur only when the calls are organised in this specific order. One notable exception is the coal tit (Periparus ater), a species that employs similar types of notes, yet does not exhibit clear order constraints within its mobbing sequences. Despite this apparent absence of order constraints, a recent experiment has demonstrated that coal tits may be sensitive to the order of notes in heterospecific calls. Therefore, the relative significance of note order in conspecific and heterospecific communication among coal tits remains unclear. We conducted a playback experiment to examine the effects of note order (natural coal tit order, typical Parid order and reversed order) and species identity (conspecific, familiar heterospecific—the great tit, Parus major, or artificial notes) on coal tit mobbing responses. Our findings indicate that coal tits exhibited a strong response to conspecific calls, regardless of the order of the notes; conversely, they displayed little to no response to heterospecific calls and artificial notes, irrespective of note order. A similar pattern was observed when assessing the general community response. This unexpectedly low response to familiar heterospecific calls may be attributable to a reduced density of great tits in the area we tested: ecological factors, such as community composition, may influence heterospecific mobbing behaviours and the subsequent biological interpretations of playback experiments. This study also underscores the necessity of conducting comparative research on closely related species to evaluate the potential generality of findings, such as strong order constraints recently observed in great tits and Japanese tits.
  • Journal article
    Cabral A, Bender IMA, Couvreur TLP, Faurby S, Hagen O, Hensen I, Kühn I, RodriguesVaz C, Sauquet H, Tobias JA, Onstein REet al., 2025,

    Seed‐dispersing vertebrates and the abiotic environment shape functional diversity of the pantropical Annonaceae

    , New Phytologist, Vol: 246, Pages: 2263-2279, ISSN: 0028-646X

    Mutualistic interactions between fruiting plants and frugivorous animals are shaped by interaction-relevant functional traits. However, it is unclear whether ‘trait matching’ underlies broad-scale relationships in plant and frugivore species and their functional diversity.We integrated novel trait data and global occurrences for c. 1900 species in a major tropical plant family (Annonaceae) with data for 7607 bird and mammal species, including 1418 frugivores, alongside data on the abiotic environment. We applied structural equation models to evaluate the direct and indirect drivers of global and continental variation in frugivory-related functional diversity in Annonaceae, and assessed frugivory-exclusive drivers through comparisons with non-frugivores.We show that global variation in Annonaceae frugivory-related functional diversity is influenced by species richness (SRic) and trait matching with co-occurring frugivorous mammals. Frugivorous birds and mammals indirectly influenced Annonaceae functional diversity at continental scales by affecting Annonaceae SRic. We found that climate, elevation, and seed dispersers jointly shaped Annonaceae diversity globally.Our results suggest that seed dispersal interactions with mammals are particularly important for shaping global variation in Annonaceae diversity, possibly through mutualistic co-evolutionary dynamics. However, distinct effects of frugivores on Annonaceae diversity across biogeographical realms suggest that biogeography modulates how mutualistic interactions promote diversity.
  • Journal article
    Anil S, Goodman DFM, Ghosh M, 2025,

    Fusing multisensory signals across channels and time

    , PLOS COMPUTATIONAL BIOLOGY, Vol: 21, ISSN: 1553-734X
  • Journal article
    Sugata K, Rahman A, Niimura K, Monde K, Ueno T, Rajib SA, Takatori M, Sakhor W, Hossain MB, Sithi SN, Jahan MI, Matsuda K, Ueda M, Yamano Y, Ikeda T, Ueno T, Tsuchiya K, Tanaka Y, Tokunaga M, Maeda K, Utsunomiya A, Okuma K, Ono M, Satou Yet al., 2025,

    Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment

    , NATURE MICROBIOLOGY, Vol: 10, ISSN: 2058-5276
  • Journal article
    Motyka M, Kusy D, Biffi G, Geiser M, Kazantsev SV, Bilkova R, Jahodarova E, Vogler AP, Bocak Let al., 2025,

    Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage (vol 39, pg 1, 2023)

    , CLADISTICS, Vol: 41, Pages: 321-321, ISSN: 0748-3007
  • Journal article
    de Souza VF, Goncalves JFDC, Rasulov B, Talts E, Morfopoulos C, Duvoisin Junior S, Albuquerque PM, Niinemets Uet al., 2025,

    Photosynthetic Temperature Tolerance Threshold Determines How Isoprene Emission is Affected by Elevated CO<sub>2</sub> Concentration at High Temperatures

    , PLANTENVIRONMENT INTERACTIONS, Vol: 6, ISSN: 2575-6265
  • Journal article
    Were VM, Yan X, Foster AJ, Sklenar J, Langner T, Gentle A, Sahu N, Bentham A, Zdrzalek R, Ryder LS, Kaimenyi DK, De La Cruz DG, Petit-Houdenot Y, Eseola AB, Smoker M, Bautista MJ, Ma W, Kourelis J, Maclean D, Banfield MJ, Kamoun S, Menke FLH, Moscou MJ, Talbot NJet al., 2025,

    The Magnaporthe oryzae effector Pwl2 alters HIPP43 localization to suppress host immunity

    , PLANT CELL, Vol: 37, ISSN: 1040-4651
  • Journal article
    Carpenter FL, Vogler AP, 2025,

    If the tape were played again: convergent evolution of clade sizes and taxonomic composition in two tropical assemblages of Coleoptera

    , ECOGRAPHY, Vol: 2025, ISSN: 0906-7590
  • Journal article
    Negi P, Pandey M, Paladi RK, Majumdar A, Pandey SP, Barvkar VT, Devarumath R, Srivastava AKet al., 2025,

    Stomata-Photosynthesis Synergy Mediates Combined Heat and Salt Stress Tolerance in Sugarcane Mutant M4209

    , PLANT CELL AND ENVIRONMENT, Vol: 48, Pages: 4668-4684, ISSN: 0140-7791
  • Journal article
    Groner VP, Cook J, Orme CDL, Amarasekare P, Comyn-Platt E, Rallings T, Joshi J, Ewers RMet al., 2025,

    Harmonizing nature's timescales in ecosystem models

    , TRENDS IN ECOLOGY & EVOLUTION, Vol: 40, Pages: 575-585, ISSN: 0169-5347
  • Journal article
    Hobbs B, Limmer N, Ossa F, Knupling E, Lenton S, Fodera V, Kalverda A, Karamanos Tet al., 2025,

    A low-complexity linker as a driver of intra- and intermolecular interactions in DNAJB chaperones

    , Nature Communications, Vol: 16, ISSN: 2041-1723

    J-domain proteins ( JDPs) act as major regulators of the proteostasis network by driving the specificity of the Hsp70 machine. Their important functions are mediated by a low-complexity glycine-/phenylalanine-rich region (GF-linker) that links the folded J-domain with the substrate binding domain. Recently, we and others have shown that in an autoinhibited JDP state, an α-helix formed within the GF-linker blocks the Hsp70 binding site on the J-domain. However, the role of the disordered GF-linker in autoinhibition and how the latter is released, are still not understood. Here, using autoinhibited DNAJB1 and DNAJB6 constructs, we show that in combination with the J-domain, the GF-linker creates a hydrophobic, partially collapsed cluster that shows a remarkable degree of long-range structural communication, disruption of which can lead to destabilisation of autoinhibition. Apart from this crucial intramolecular role, we reveal that the GF-linker can also be recognised by the substrate-binding domain of Hsp70 and dictate the lifetime of the entire JDP–Hsp70 complex. Strikingly, the GF-linkers of DNAJB1 and DNAJB6 display distinct structural properties that lead to different Hsp70 binding kinetics, showing that the behaviour of the GF-linker can vary dramatically even within the same class of JDPs.
  • Journal article
    Zhang H, Wang H, Wright IJ, Prentice IC, Harrison SP, Smith NG, Westerband AC, Rowland L, Plavcova L, Morris H, Reich PB, Jansen S, Keenan T, Nguyen NBet al., 2025,

    Thermal acclimation of stem respiration implies a weaker carbon-climate feedback

    , Science, ISSN: 0036-8075
  • Journal article
    Kim J, Darlington A, Muñoz-Montero S, Montenegro R, Herrera-Martín N, Dalby P, Banks A, Prakash S, Polizzi K, Bates D, Jimenez Zarco Jet al., 2025,

    Gene expression depends on the interplay among growth, resource biogenesis, and nutrient quality

    , ACS Synthetic Biology, ISSN: 2161-5063

    The gene expression capacity of bacteria depends on the interplay between growth and the availability of the transcriptional and translational machinery. Growth rate is accepted as the physiological parameter controlling the allocation of cellular resources. Understanding the relationship between growth and resources is key for the efficient design of genetic constructs, but it is obscured by the mutual dependence between growth and gene expression. In this work, we investigate the contributions of molecular factors, growth rate, and metabolism to gene expression by investigating the behavior of bacterial cells grown in chemostats. Using a model of the whole cell and validating it experimentally, our results show that while growth rate and molecular factors, such as the number of rRNA operons, set the abundance of transcriptional and translational machinery, it is metabolism that governs the usage of resources by tuning elongation rates. We show, using a biotechnologically relevant example, that gene expression capacity can be maximized using low growth in a high-quality medium. These findings unveil fundamental trade-offs in physiology that will inform future bioprocess optimization.
  • Journal article
    Little TS, Cunningham DA, Christophides GK, Reid AJ, Langhorne Jet al., 2025,

    De novo assembly of <i>plasmodium interspersed repeat</i> (<i>pir</i>) genes from <i>Plasmodium vivax</i> RNAseq data suggests geographic conservation of sub-family transcription

    , BMC GENOMICS, Vol: 26, ISSN: 1471-2164
  • Journal article
    Duchêne DA, Chowdhury A-A, Yang J, Iglesias-Carrasco M, Stiller J, Feng S, Bhatt S, Gilbert MTP, Zhang G, Tobias JA, Ho SYWet al., 2025,

    Drivers of avian genomic change revealed by evolutionary rate decomposition

    , Nature, Vol: 641, Pages: 1208-1216, ISSN: 0028-0836

    Modern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change1,2,3,4, but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds5,6, we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous–Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.
  • Journal article
    Sauthof L, Szczepek M, Schmidt A, Bhowmick A, Dasgupta M, Mackintosh MJ, Gul S, Fuller FD, Chatterjee R, Young ID, Michael N, Heyder NA, Bauer B, Koch A, Bogacz I, Kim I-S, Simon PS, Butryn A, Aller P, Chukhutsina VU, Baxter JM, Hutchison CDM, Liebschner D, Poon B, Sauter NK, Miller MD, Phillips Jr GN, Alonso-Mori R, Hunter MS, Batyuk A, Owada S, Tono K, Tanaka R, van Thor JJ, Krauss N, Lamparter T, Brewster AS, Schapiro I, Orville AM, Yachandra VK, Yano J, Hildebrandt P, Kern JF, Scheerer Pet al., 2025,

    Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

    , SCIENCE ADVANCES, Vol: 11
  • Journal article
    Yu X, Nollet M, Franks N, Wisden Wet al., 2025,

    Sleep and the recovery from stress

    , Neuron, ISSN: 0896-6273

    The relationship between stress and sleep is multifaceted, with stress capable of both disrupting and promoting sleep depending on the nature, intensity, and duration of the stressor. While stress commonly leads to sleep fragmentation and arousal in both humans and animals, certain selective stressors, such as immune challenges and psychosocial stress, promote sleep in rodent models. Specific neural circuits, such as those involving the ventral tegmental area and lateral habenula, mediate this stress-induced sleep. Post-stress sleep may facilitate recovery, reduce anxiety, and enhance stress resilience, but the extent to which sleep versus wakefulness post-stress aids long-term adaptation is unclear. Both human and animal studies highlight a bidirectional relationship, where stress-induced changes in sleep architecture may have adaptive or maladaptive consequences. Here, we propose that post-stress sleep contributes to resilience and discuss potential mechanisms underlying this process. A deeper understanding of these pathways may provide new strategies for enhancing stress recovery and improving mental health outcomes.
  • Journal article
    Pringle S, Dallimer M, Goddard MA, Le Goff LK, Hart E, Langdale SJ, Fisher JC, Abad S-A, Ancrenaz M, Angeoletto F, Auat Cheein F, Austen GE, Bailey JJ, Baldock KCR, Banin LF, Banks-Leite C, Barau AS, Bashyal R, Bates AJ, Bicknell JE, Bielby J, Bosilj P, Bush ER, Butler SJ, Carpenter D, Clements CF, Cully A, Davies KF, Deere NJ, Dodd M, Drinkwater R, Driscoll DA, Dutilleux G, Dyrmann M, Edwards DP, Farhadinia MS, Faruk A, Field R, Fletcher RJ, Foster CW, Fox R, Francksen RM, Franco AMA, Gainsbury AM, Gardner CJ, Giorgi I, Griffiths RA, Hamaza S, Hanheide M, Hayward MW, Hedblom M, Helgason T, Heon SP, Hughes KA, Hunt ER, Ingram DJ, Jackson-Mills G, Jowett K, Keitt TH, Kloepper LN, Kramer-Schadt S, Labisko J, Labrosse F, Lawson J, Lecomte N, de Lima RF, Littlewood NA, Marshall HH, Masala GL, Maskell LC, Matechou E, Mazzolai B, McConnell A, Melbourne BA, Miriyev A, Nana ED, Ossola A, Papworth S, Parr CL, Payo-Payo A, Perry G, Pettorelli N, Pillay R, Potts SG, Prendergast-Miller MT, Qie L, Rolley-Parnell P, Rossiter SJ, Rowcliffe M, Rumble H, Sadler JP, Sandom CJ, Sanyal A, Schrodt F, Sethi SS, Shabrani A, Siddall R, Smith SC, Snep RPH, Soulsbury CD, Stanley MC, Stephens PA, Stephenson PJ, Struebig MJ, Studley M, Svátek M, Tang G, Taylor NK, Umbers KDL, Ward RJ, White PJC, Whittingham MJ, Wich S, Williams CD, Yakubu IB, Yoh N, Zaidi SAR, Zmarz A, Zwerts JA, Davies ZGet al., 2025,

    Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age

    , Nature Ecology & Evolution, ISSN: 2397-334X

    With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more ‘difficult’ taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.
  • Report
    Moustafa N, Saenz Cavazos P, Beath H, Morris O, Liu E, Morimoto Y, Muuls M, Nishide A, Pearse W, Rogelj J, Rolandi T, Shah N, Taylor Pet al., 2025,

    Destination Net-Zero: what is your best path? Insights for decision-makers navigating the low carbon transition
  • Journal article
    McArthur HCW, Bajur AT, Iliopoulou M, Spillane Ket al., 2025,

    Antigen mobility regulates the dynamics and precision of antigen capture in the B cell immune synapse

    , Proceedings of the National Academy of Sciences of USA, Vol: 122, ISSN: 0027-8424

    B cells discriminate antigens in immune synapses by capturing them from antigen-presenting cells (APCs). This discrimination relies on the application of mechanical force to B cell receptor (BCR)-antigen bonds, allowing B cells to selectively disrupt low-affinity interactions while internalizing high-affinity antigens. Using DNA-based tension sensors combined with high-resolution imaging, we demonstrate that the magnitude, location, and timing of forces within the immune synapse are influenced by the fluidity of the antigen-presenting membrane. Transitioning antigens from a high-mobility to a low-mobility substrate significantly increases the probability and speed of antigen extraction while also improving affinity discrimination. This shift in antigen mobility also reshapes the synapse architecture, altering spatial patterns of antigen uptake. Despite these adaptations, B cells maintain consistent levels of proximal and downstream signaling pathway activation regardless of antigen mobility. They also efficiently transport internalized antigens to major histocompatibility complex class II (MHCII)-positive compartments for processing. These results demonstrate that B cells mount effective responses to antigens across diverse physical environments, though the characteristics of that environment may influence the speed and accuracy of B cell adaptation during an immune response.
  • Journal article
    Alonso A, Kirkegaard JB, Endres RG, 2025,

    Persistent pseudopod splitting is an effective chemotaxis strategy in shallow gradients

    , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 122, ISSN: 0027-8424
  • Journal article
    Yesilyurt-Dirican ZE, Qi C, Wang Y-C, Simm A, Deelen L, Gasim AHA, Lewis-McDougall F, Ellison-Hughes GMet al., 2025,

    SGLT2 inhibitors as a novel senotherapeutic approach

    , NPJ AGING, Vol: 11
  • Conference paper
    Xu V, Barritt J, Bubeck D, Wake M, Rouse Set al., 2025,

    Countdown to Package: Molecular Insights into the Rep-mediated Adenoassociated-virus Packaging Machinery

    , 28th Annual Meeting of the American-Society-of-Gene-and-Cell-Therapy (ASGCT), Publisher: CELL PRESS, ISSN: 1525-0016
  • Journal article
    Rice AJ, Sword TT, Chengan K, Mitchell DA, Mouncey NJ, Moore SJ, Bailey CBet al., 2025,

    Cell-free synthetic biology for natural product biosynthesis and discovery

    , CHEMICAL SOCIETY REVIEWS, Vol: 54, Pages: 4314-4352, ISSN: 0306-0012
  • Journal article
    Kim TD, Pretorius D, Murray JW, Cardona Tet al., 2025,

    Exploring the structural diversity and evolution of the D1 subunit of photosystem II using AlphaFold and Foldtree

    , Physiologia Plantarum, Vol: 177, ISSN: 0031-9317

    Although our knowledge of photosystem II has expanded to include time-resolved atomic details, the diversity of experimental structures of the enzyme remains limited. Recent advances in protein structure prediction with AlphaFold offer a promising approach to fill this gap in structural diversity in non-model systems. This study used AlphaFold to predict the structures of the D1 protein, the core subunit of photosystem II, across a broad range of photosynthetic organisms. The prediction produced high-confidence structures, and structural alignment analyses highlighted conserved regions across the different D1 groups, which were in line with high pLDDT scoring regions. In contrast, varying pLDDT in the DE loop and terminal regions appears to correlate with different degrees of structural flexibility or disorder. Subsequent structural phylogenetic analysis using Foldtree provided a tree that is in good agreement with previous sequence-based studies. Moreover, the phylogeny supports a parsimonious scenario in which far-red D1 and D1INT evolved from an ancestral form of G4 D1. This work demonstrates the potential of AlphaFold and Foldtree to study the molecular evolution of photosynthesis.
  • Journal article
    Lieb ZE, Meijaard E, Brodie JF, Shabrani A, Mohd-Azlan J, Supriatna J, Struebig MJ, Deere NJ, Spencer KL, Heon S, Wong LJ, Juiling S, Hearn A, Coudrat CNZ, Jati AS, Linkie M, Ngoprasert D, Das D, Wearn OR, Gray RJ, Cabanas AJC, Chankhao A, Saisamorn A, Azhar B, Lee BPYH, Goossens B, Traeholt C, MacDonald DW, Lastica-Ternura EA, Garcia-Gil F, Pattiselanno F, Fredriksson G, Davies G, Hilser H, Wheelhouse J, van der Ploeg J, Redeña-Santos JC, Moore JM, Parakkasi K, Berman LM, Lee SXT, Hughes LJ, Alen LH, Ancrenaz M, Chua MAH, Handschuh M, Ward M, Rifqi MA, Bin Jaini MA, Bin Omar MS, Pongpattananurak N, Shwe NM, Daniel OZ, Sinovas P, Deka P, Radinal, Thaung R, Ewers RM, Legrand R, Sukmasuang R, Kaicheen SS, Khalid S, Aung SS, Sheherazade S, Davies SJ, Braasch T, Gray TNE, Redford T, Grafe U, Song X, Luskin MSet al., 2025,

    Mapping multiple wild pig species’ population dynamics in southeast asia during the african swine fever outbreak (2018–2024)

    , Conservation Letters, Vol: 18, ISSN: 1755-263X

    The 2018 arrival of African swine fever (ASF) in China was followed by reports of wild pig deaths across most countries in Southeast Asia. However, the magnitude and duration of population-level impacts of ASF on wild pig species remain unclear. To elucidate the spatiotemporal spread of ASF in the region for native pig species, we gathered qualitative information on wild pig population dynamics in Southeast Asia between 2018 and 2024 from 88 expert elicitation questionnaires representing sites in 11 countries. Peak reported population declines occurred in 2021 and 2022, with more than half of respondents reporting declining wild pig populations, far higher than in earlier years. The reported declines waned to 44.23% in 2024, whereas simultaneously, the number of populations reported to be “increasing” increased from 11.3%–13.2% in 2019–2022 to 28.9% in 2024. These reports suggest that the ASF outbreak may have peaked for wild boars and bearded pigs in mainland Southeast Asia, Borneo, and Sumatra, with some subsequent recovery. However, the disease is still expanding into the ranges of island endemic species, such as new reports for the Sulawesi warty pig (Sus celebensis) in September of 2024. Island endemics remain particularly vulnerable to extinction from ASF and require urgent monitoring and conservation action.

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