Article
Biochemistry & Molecular Biology
Cristobal Gallegos, Kathryn A. Hodgins, Keyne Monro
Summary: Climate change is causing species ranges to shift and affect their adaptability and vulnerability. Understanding current species distributions, adaptive variants, and their distribution in rapidly changing landscapes is crucial for predicting responses to future climates and conservation strategies. However, this knowledge is lacking for many endangered species. In this study, we analyze the genetic variation, climate adaptation and vulnerability of two sister species of marine tubeworms in a climate change-sensitive region. Our findings indicate genetic isolation, contrasting signals of thermal adaptation, and differing risks of maladaptation under future temperatures across their ranges. These results have implications for understanding local adaptation, guiding conservation planning in coastal ecosystems, and validating experimental predictions.
Article
Biochemistry & Molecular Biology
Clement Gain, Benedicte Rhone, Philippe Cubry, Israfel Salazar, Florence Forbes, Yves Vigouroux, Flora Jay, Olivier Francois
Summary: Genomic offset statistics can predict population maladaptation to rapid habitat alteration, but they have limitations. We proposed a geometric measure to predict fitness after rapid change in the local environment and verified our theory with computer simulations and empirical data. This research provides a theoretical foundation for the potential application of genomic offset statistics in conservation management.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Eleanor C. Sheppard, Claudia A. Martin, Claire Armstrong, Catalina Gonzalez-Quevedo, Juan Carlos Illera, Alexander Suh, Lewis G. Spurgin, David S. Richardson
Summary: Understanding the mechanisms and genes that enable animals to adapt to pathogens is crucial. This study explores the genetic variation associated with avian pox infection in Berthelot's pipit populations. At the individual level, there was no evidence of variation in MHC class I and TLR4 being associated with pox infection. However, at the population-level, strong associations were found between avian pox prevalence and allele frequencies of SNPs located within genes involved in stress signalling and immune responses.
Article
Evolutionary Biology
Frederik Van Daele, Olivier Honnay, Hanne De Kort
Summary: Climate change affects temperate forest ecosystems, but many forest herbs may not be able to adapt due to dispersal limitation. Assisted migration strategies can help herbs with low adaptive capacity, but they often overlook evolutionary constraints. This study examines the local adaptation and vulnerability of the forest herb Primula elatior to climate change using genomic analysis. It concludes that assisted migration from southern populations may be risky due to nonclimatic maladaptation and low adaptive capacity.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Evolutionary Biology
Christian Rellstab, Benjamin Dauphin, Moises Exposito-Alonso
Summary: The concept of genomic offset combines genomic and environmental data to assess a population's adaptation to new environmental conditions. While promising, it requires careful consideration of risks and limitations, and should be used in conjunction with other approaches for informing conservation measures.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Biodiversity Conservation
Remi Tournebize, Leyli Borner, Stephanie Manel, Christine N. Meynard, Yves Vigouroux, Dominique Crouzillat, Coralie Fournier, Mohamed Kassam, Patrick Descombes, Christine Tranchant-Dubreuil, Hugues Parrinello, Catherine Kiwuka, Ucu Sumirat, Hyacinthe Legnate, Jean-Leon Kambale, Bonaventure Sonke, Jose Cassule Mahinga, Pascal Musoli, Steven B. Janssens, Piet Stoffelen, Alexandre de Kochko, Valerie Poncet
Summary: The assessment of population vulnerability under climate change is crucial for planning conservation and ensuring food security. Comparing ecological and genomic vulnerabilities within the species' native range reveals insights about habitat loss and adaptive potential. Research on Coffea canephora (Robusta) found that suitable habitat would decrease by half by 2050 and populations in West Africa and the DRC-Uganda border region have higher genomic vulnerability.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Evolutionary Biology
Heng Yang, Jialiang Li, Richard Ian Milne, Wenjing Tao, Yi Wang, Jibin Miao, Wentao Wang, Tsam Ju, Sonam Tso, Jian Luo, Kangshan Mao
Summary: Habitat loss induced by climate warming is a major threat to biodiversity, particularly to threatened species. This study focuses on Cupressus gigantea to understand its genetic diversity and distributional responses to climate change. The research identifies separate management units based on genetic clusters and demographic histories, and highlights the vulnerability of all populations of C. gigantea to future climate change.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Environmental Sciences
Marina Andrijevic, Carl-Friedrich Schleussner, Jesus Crespo Cuaresma, Tabea Lissner, Raya Muttarak, Keywan Riahi, Emily Theokritoff, Adelle Thomas, Nicole van Maanen, Edward Byers
Summary: Most global climate change models and policies do not take into account adaptation or societies' ability to adapt. The authors propose integrating adaptation into these models using the Shared Socioeconomic Pathway scenario framework and quantifying adaptive capacity through socioeconomic indicators. Adaptation needs and capacities vary across regions and are not adequately represented in current global models. The proposed approach provides a way to assess adaptive capacity and deliver relevant information for realistic assessment of climate risks and reduction strategies.
NATURE CLIMATE CHANGE
(2023)
Article
Multidisciplinary Sciences
Lisa Bjerregaard Jorgensen, Michael Orsted, Hans Malte, Tobias Wang, Johannes Overgaard
Summary: This study found that the rate of biological processes in the permissive temperature range increases by 7% per degree Celsius, while the heat failure rate is extremely temperature sensitive within the stressful temperature range. The projected increase in the frequency and intensity of heatwaves may exacerbate heat mortality for ectothermic species.
Article
Multidisciplinary Sciences
Tin Hang Hung, Thea So, Bansa Thammavong, Voradol Chamchumroon, Ida Theilade, Chhang Phourin, Somsanith Bouamanivong, Ida Hartvig, Hannes Gaisberger, Riina Jalonen, David H. Boshier, John J. MacKay
Summary: Rosewoods have been highly trafficked in the illegal wildlife trade since 2005. The two most sought-after species, Dalbergia cochinchinensis and Dalbergia oliveri, face significant genetic risks and limited adaptability knowledge, hindering conservation efforts. This study found differential adaptive genomic variation in response to temperature and precipitation-related variables between the two species, suggesting the need for species-specific conservation actions. The research also developed a seed source matching application to aid restoration efforts. Overall, this ecological genomic research is important for global tropical tree conservation and mitigating climate change risks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Environmental Sciences
Alexandre K. Magnan, Robert Bell, Virginie K. E. Duvat, James D. Ford, Matthias Garschagen, Marjolijn Haasnoot, Carmen Lacambra, Inigo J. Losada, Katharine J. Mach, Melinda Noblet, Devanathan Parthasaranthy, Marcello Sano, Katharine Vincent, Ariadna Anisimov, Susan Hanson, Alexandra Malmstrom, Robert J. Nicholls, Gundula Winter
Summary: The state of global coastal adaptation is currently halfway towards its full potential, with urban areas generally scoring higher than rural areas. Efforts in adaptation are unbalanced across different dimensions and strategizing for long-term pathways is limited. This assessment provides a multi-dimensional and locally grounded perspective on global coastal adaptation, highlighting the need to refine global adaptation targets and identify priorities transcending development levels.
NATURE CLIMATE CHANGE
(2023)
Article
Urban Studies
Salvatore Paolo De Rosa, Joost de Moor, Marwa Dabaieh
Summary: Climate change adaptation in cities has often neglected the root causes of unequal vulnerability, leading to climate injustices. Existing studies have focused on positive cases and have not explored why these issues are not politicized. This research investigates the role of political outsiders in politicizing urban climate adaptation and finds that climate movements often ignore local adaptation while social justice activism has untapped potential to support transformational adaptation.
Article
Genetics & Heredity
Yihan Wang, Lin Zhang, Yuchao Zhou, Wenxin Ma, Manyu Li, Peng Guo, Li Feng, Chengxin Fu
Summary: Understanding the adaptive genetic variation and vulnerabilities of plant populations to climate change is crucial for biodiversity preservation and management interventions. Landscape genomics can be a cost-effective approach to investigate the molecular signatures underlying local adaptation. This study focused on Tetrastigma hemsleyanum, a perennial herb in subtropical China, and used landscape genomics to explore its genomic variation across climate gradients and vulnerability to future climate change. The findings revealed that climatic variation explained more genomic variation than geographical distance, highlighting the importance of local adaptation to heterogeneous environments. The study also identified candidate adaptive genetic markers associated with flowering time and plant response to abiotic stresses, providing valuable insights for breeding and agricultural practices. Additionally, the study emphasized the high genomic vulnerability of T. hemsleyanum to climate change in certain regions and advocated for proactive management efforts. Overall, this research provides robust evidence of local climate adaptation and enhances our understanding of adaptation in herbs in subtropical China.
FRONTIERS IN GENETICS
(2023)
Article
Development Studies
Qin Li, Lei Zhu, Xunpeng Shi
Summary: This study assesses the vulnerability and adaptation of China's provinces to climate change by employing a combination of the criteria importance intercriteria correlation method and Grey relational analysis. The study reveals significant disparities in the levels of adaptation and vulnerability across regions and highlights the key role of ecological and energy system transition in facilitating adaptation to climate change.
SUSTAINABLE DEVELOPMENT
(2023)
Article
Nutrition & Dietetics
Dachuan Liu, Yan Li, Pengfei Wang, Huaqi Zhong, Pu Wang
Summary: The agricultural systems in northwest China are highly vulnerable to the impacts of climate change, with extreme climate disasters and increased pests and weeds posing significant challenges. In order to adapt and mitigate these impacts, key strategies include optimizing agricultural geographic distribution, cultivating new crop varieties, adjusting cropping practices, developing water-saving irrigation systems, enhancing disaster prevention and mitigation capabilities, and strengthening scientific and human resources.
FRONTIERS IN NUTRITION
(2021)
Article
Forestry
Saeid Ghasemi Esfahlan, Roghayeh Hemmati, Shohreh Mohebbi, Jacqueline Batley, Mahdi Arzanlou
Summary: Trunk disease is a major problem on grapevine in Zanjan province, and the causes of the decline are still unknown. This study investigated factors related to grapevine decline in vineyards of Zanjan province. Fungal isolates were collected and identified, with Phaeoacremonium minimum, Microsphaeropsis olivacea, and Kalmusia variispora identified as the dominant species and main trunk pathogens in the region.
Article
Plant Sciences
Rosalie J. Harris, Callum Bryant, Melinda A. Coleman, Andrea Leigh, Veronica F. Briceno, Pieter A. Arnold, Adrienne B. Nicotra
Summary: Foundation seaweed species are declining and facing extinctions due to unstable sea surface temperatures. Existing methods for characterizing seaweed thermal tolerance are time-consuming and hinder comparisons between species. A new method using temperature-dependent fluorescence curves offers a high-throughput approach for rapidly assessing photosynthetic thermal tolerance of seaweeds.
JOURNAL OF PHYCOLOGY
(2023)
Article
Environmental Sciences
Tanika C. Shalders, Curtis Champion, Melinda A. Coleman, Peter Butcherine, Matt K. Broadhurst, Bryan Mead, Kirsten Benkendorff
Summary: Ocean warming and marine heatwaves can impact the nutritional quality of harvested marine resources, but the effects of different exposure durations and temperatures are not well understood. In this study, the nutritional quality of eastern school prawns was tested after short-term and longer-term exposures to projected ocean-warming temperatures and marine heatwaves. Results showed that the nutritional quality of the prawns remained resilient after short-term exposure, but changed after longer-term exposure. Additionally, the study highlighted the importance of exposure duration and sampling time in measuring the nutritional response of the species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Plant Sciences
Mark C. C. Derbyshire, Jacob Marsh, Soodeh Tirnaz, Henry T. T. Nguyen, Jacqueline Batley, Philipp E. E. Bayer, David Edwards
Summary: This study analyzes the soybean pangenome to identify fatty acid biosynthesis genes and their sequence diversity. It finds possible instances of gene missing in wild soybean and identifies missense variants in fatty acid biosynthesis genes. The frequency of these variants has been significantly reduced during domestication.
Article
Environmental Sciences
Monica F. Danilevicz, Roberto Lujan Rocha, Jacqueline Batley, Philipp E. Bayer, Mohammed Bennamoun, David Edwards, Michael B. Ashworth
Summary: Narrow-leafed lupin is an important dryland crop, but it is challenging to control the closely related sandplain lupin, which reduces yield and quality. A segmentation model was trained using deep learning to detect sandplain lupins and differentiate them from narrow-leafed lupins under field conditions.
Article
Plant Sciences
Aldrin Y. Cantila, William J. W. Thomas, Nur Shuhadah Mohd Saad, Anita A. Severn-Ellis, Robyn Anderson, Philipp E. Bayer, David Edwards, Angela P. van de Wouw, Jacqueline Batley
Summary: Utilising resistance genes, such as LepR1, could help manage blackleg disease in canola and increase crop yield. A genome wide association study in canola revealed significant SNPs associated with LepR1 resistance, with the majority located on chromosome A02 and containing multiple resistance gene analogs. This research provides insights into blackleg resistance in canola and aids in the identification of functional LepR1 candidate genes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Andrew Chen, Jiaman Sun, Guillaume Martin, Lesley-Ann Gray, Eva Hribova, Pavla Christelova, Nabila Yahiaoui, Steve Rounsley, Rebecca Lyons, Jacqueline Batley, Ning Chen, Sharon Hamill, Subash K. Rai, Lachlan Coin, Brigitte Uwimana, Angelique D'Hont, Jaroslav Dolezel, David Edwards, Rony Swennen, Elizabeth A. B. Aitken
Summary: In this study, the resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) in Musa acuminata ssp. malaccensis was characterized. QTL-seq analysis of an F2 population segregating for resistance revealed a major QTL on the long arm of chromosome 3. This research provides a foundation for marker assisted selection in breeding programs and identification of resistance genes.
Article
Microbiology
Andrew Chen, Jiaman Sun, Altus Viljoen, Diane Mostert, Yucong Xie, Leroy Mangila, Sheryl Bothma, Rebecca Lyons, Eva Hribova, Pavla Christelova, Brigitte Uwimana, Delphine Amah, Stephen Pearce, Ning Chen, Jacqueline Batley, David Edwards, Jaroslav Dolezel, Peter Crisp, Allan F. Brown, Guillaume Martin, Nabila Yahiaoui, Angelique D'Hont, Lachlan Coin, Rony Swennen, Elizabeth A. B. Aitken
Summary: Fusarium wilt of banana is a destructive disease that has caused significant damage to banana production worldwide. In this study, the genetic basis of host resistance to the causal agent Fusarium oxysporum f. sp. Cubense (Foc) is dissected using two segregating populations. Marker loci and trait association analysis revealed a specific genetic interval associated with resistance on chromosome 3. The expression of pattern recognition receptors was found to be rapidly upregulated in resistant progenies, suggesting their involvement in resistance. The developed markers can aid breeding programs in selecting for resistance to Foc.
Article
Biotechnology & Applied Microbiology
Junrey C. C. Amas, Philipp E. E. Bayer, Wei Hong Tan, Soodeh Tirnaz, William J. W. Thomas, David Edwards, Jacqueline Batley
Summary: This study utilized the B. rapa pangenome to identify a comprehensive repertoire of RGAs in B. rapa. It found that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. Comparative analysis with B. napus revealed significant RGA conservation between the two species. The study also identified candidate RGAs located within known B. rapa disease resistance QTL and clarified the genetic relationship of blackleg resistance genes.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Agronomy
Angela P. Van de Wouw, Jack L. Scanlan, Hawlader A. Al-Mamun, Marie-Helene Balesdent, Lydia Bousset, Lenka Burketova, Luis del Rio Mendoza, W. G. Dilantha Fernando, Coreen Franke, Barbara J. Howlett, Yong-Ju Huang, E. Eirian Jones, Birger Koopmann, Suhaizan Lob, Ali Z. Mirabadi, Bridgit C. Nugent, Gary Peng, Franco R. Rossi, Huibrecht Schreuder, Annie R. Tabone, Gert J. Van Coller, Jacqueline Batley, Alexander Idnurm
Summary: This study collected isolates of Leptosphaeria maculans and L. biglobosa from different countries to represent the global diversity of these fungal pathogens. The genomes of L. maculans isolates were sequenced, and the distribution and identity of avirulence gene alleles were determined. The study found geographical separation of populations within L. maculans isolates, providing a resource for studying disease-causing mechanisms and discovering new resistance traits.
Article
Agronomy
Aldrin Y. Cantila, William J. W. Thomas, Philipp E. Bayer, David Edwards, Jacqueline Batley
Summary: This study predicts and identifies the number and function of TM-CC genes in Brassicaceae plants, and suggests that they may play a significant role in disease resistance. It provides a valuable resource for the study of TM-CCs and their potential functional involvement in resistance.
Article
Plant Sciences
Cassandria G. Tay G. Fernandez, Philipp E. Bayer, Jakob Petereit, Rajeev Varshney, Jacqueline Batley, David Edwards
Summary: Many genome annotations contain false-positive gene models, which can lead to errors in phylogenetic and comparative studies. In this study, a method based on evolutionary conservation is proposed to predict gene models and identify potentially erroneous annotations. A set of 15,345 representative gene models from 12 legume assemblies is developed using this method, which can support genome annotations for other legumes.
Article
Remote Sensing
Wijayanti Nurul Khotimah, Mohammed Bennamoun, Farid Boussaid, Lian Xu, David Edwards, Ferdous Sohel
Summary: Transformers have been successful in computer vision tasks due to their ability to capture long-range feature dependencies. However, for hyperspectral data classification, capturing both short and long-range band dependencies is important. To address this, a convolution-transformer (conformer) based framework called MCE-ST is proposed. MCE-ST combines the strengths of transformers and CNNs by using a convolution-based tokenization method and a multiscale conformer encoder.
INTERNATIONAL JOURNAL OF APPLIED EARTH OBSERVATION AND GEOINFORMATION
(2023)
Article
Biotechnology & Applied Microbiology
Jian Wang, Wu Yang, Shaohong Zhang, Haifei Hu, Yuxuan Yuan, Jingfang Dong, Luo Chen, Yamei Ma, Tifeng Yang, Lian Zhou, Jiansong Chen, Bin Liu, Chengdao Li, David Edwards, Junliang Zhao
Summary: The researchers developed a novel strategy and analysis pipeline for constructing a plant pangenome and identifying the position information of genetic variants. They successfully constructed a high-quality rice pangenome and identified causal structural variations related to rice grain weight and plant height. This study provides valuable genomic resources for rice genomics research and improvement.