Article
Plant Sciences
Yifei Wang, Fang Wen, Xin Hong, Zhenglong Li, Yaolei Mi, Bo Zhao
Summary: In this study, the complete chloroplast genomes of twelve Paraboea species were sequenced and analyzed, revealing the genomic structure and composition, as well as potential molecular markers. In the phylogenetic tree, all Paraboea species formed a distinct clade, confirming their monophyly. Additionally, genes related to photosynthesis and protein synthesis were found to play crucial roles in the adaptability of Paraboea to diverse karst environments.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Guangya Xu, Weirong Xu
Summary: This study analyzed the complete chloroplast genomes of Chinese wild Vitis species, revealing distinct evolutionary histories and geographic origins among East Asian, Eurasian, and North American species. Molecular clock analysis indicated a possible origin of Vitis species and gene pool in southern China during the Pleistocene period, with cold-adapted subspecies able to colonize new habitats due to climate fluctuations. These findings shed light on the adaptive radiation of Chinese wild Vitis species in diverse environments.
Article
Plant Sciences
Xiaomin Wang, Shengyi Bai, Zhaolei Zhang, Fushun Zheng, Lina Song, Lu Wen, Meng Guo, Guoxin Cheng, Wenkong Yao, Yanming Gao, Jianshe Li
Summary: In this study, the chloroplast genomes of 29 tomato germplasms were sequenced and analyzed to compare and understand their phylogenetic relationships. The analysis revealed highly conserved characteristics among the cp genomes, including structure, gene and intron number, inverted repeat regions, and repeat sequences. Candidate SNP markers for future studies were selected based on highly polymorphic SNP loci. The phylogenetic tree showed that the cp genomes of tomatoes were clustered into two major clades, with S. pimpinellifolium and S. lycopersicum showing a close genetic relationship. Only rps15 gene exhibited the highest average K-A/K-S ratio in the analysis of adaptive evolution, indicating strong positive selection. This study provides valuable information for further research on phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Computer Science, Artificial Intelligence
Bowu Jiang, Wenkai Lu
Summary: In seismic exploration, surface-related multiple elimination (SRME) is an important algorithm that aims to remove multiples while preserving primaries. Curvelet-based AMS methods have shown outstanding performances in processing seismic data, and an accelerated ICT method has been proposed to improve efficiency.
IEEE TRANSACTIONS ON IMAGE PROCESSING
(2021)
Article
Multidisciplinary Sciences
Bao-Lin Zhang, Wu Chen, Zefu Wang, Wei Pang, Meng -Ting Luo, Sheng Wang, Yong Shao, Wen-Qiang He, Yuan Deng, Long Zhou, Jiawei Chen, Min -Min Yang, Yajiang Wu, Lu Wang, Hugo Fernandez-Bellon, Sandra Molloy, Helene Meunler, Fanelie Wanert, Lukas Kuderna, Tomas Marques-Bonet, Christian Roos, Xiao-Guang Qi, Ming Li, Zhiji Liu, Mikkel Heide Schierup, David N. Cooper, Jianquan Liu, Yong-Tang Zheng, Guojie Zhang, Dong-Dong Wu
Summary: Through phylogenomic analysis of 12 macaque species, we discovered that the fascicularis group originated from an ancient hybridization event between the sinica and silenus groups around 3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions showed equal contributions from each parental lineage, suggesting their importance in maintaining hybrid integrity. We also identified reproduction-associated genes and confirmed susceptibility to HIV-1 infection in all extant Western silenus species. Our study provides new insights into macaque evolution and highlights a rare hybrid speciation event in primates.
Article
Biochemistry & Molecular Biology
Benoit Perez-Lamarque, Guilhem Sommeria-Klein, Lorena Duret, Helene Morlon
Summary: This article discusses the evolution of host-associated microbial communities as their hosts diversify. It explores the conservation of their composition, the composition of ancestral microbiota, and the covariation of microbial taxa abundance over millions of years. The study employs multivariate phylogenetic models and extends these models to estimate phylosymbiosis, ancestral microbiota composition, and integration of bacterial abundances.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Nanzhen Qiao, Julia Bechtner, Margo Cnockaert, Eliza Depoorter, Christian Diaz-Munoz, Peter Vandamme, Luc De Vuyst, Michael G. Ganzle
Summary: This study characterized the genus Periweissella through phylogenetic analysis and genomic analysis, revealing its evolutionary relationship with closely related genera Weissella and Furfurilactobacillus. The study also determined the genetic and physiological traits of the genus. Results showed that Periweissella is the link between rod-shaped heterofermentative lactobacilli and the coccoid Leuconostoc clade, and it is the only heterofermentative genus in the Lactobacillaceae that comprises predominantly motile strains.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Plant Sciences
Dhafer A. Alzahrani, Enas J. Albokhari, Samaila S. Yaradua, Abidina Abba
Summary: This study presents the complete chloroplast genomes of four medicinal species in the Capparaceae family from two different genera for the first time, providing resources for studying their evolutionary process and inferring their phylogenetic positions. The chloroplast genomes of these species contain unique genes and variable hotspot regions that can be used as molecular markers for species authentication and phylogenetic studies. The phylogenetic relationships among these species and their positions within the Brassicales order are highly supported by the relationships in the phylogenetic tree.
Editorial Material
Biochemistry & Molecular Biology
Breda Zunkovic, Markus Schmidt
Summary: A new study reveals that bird pupillary responses during sleep are opposite to those seen in mammals, highlighting the diverse adaptive nature of sleep across different species.
Article
Biology
Claire A. McLean, Jane Melville, Joseph Schubert, Rebecca Rose, Iliana Medina
Summary: Changes in fire regimes due to human activities have an impact on spider populations, with shorter fire intervals posing a threat to certain species. Fire also affects the abundance and composition of spider species in forests compared to other vegetation types. Functional traits may influence how spiders respond to fire, with orb and sheet web weavers being more likely to be absent after fire.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Engineering, Chemical
Le Wang, Andong Qi, Jianguang Liu, Yan Shen, Jinshui Wang
Summary: The novel strain Candida tropicalis Y31-N with high tolerance against furfural was obtained through continuous domestication processes from the parent strain Candida tropicalis Y-3. The Y31-N showed a significant increase in xylitol yield and furfural consumption rate compared to Y-3. It was able to control membrane fluidity and maintain membrane integrity by regulating fatty acid composition, as well as rapidly produce ATP and NAD(P)H to alleviate furfural stress through metabolic rearrangement. Furthermore, several genes related to trehalose synthesis, GABA metabolism, and NADPH production were identified as essential for furfural resistance through single-gene knockout. This study contributes to a better understanding of the mechanisms of furfural tolerance and provides insights for future metabolic engineering.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Plant Sciences
Zheng-Ren Zhang, Xue Yang, Wei-Ying Li, Yan-Qiong Peng, Jie Gao
Summary: In this study, the chloroplast genomes of various Ficus species were sequenced and analyzed, revealing a conserved genomic structure and the presence of unique genes. The phylogenetic relationships of Ficus were found to be complex, and divergence among species likely occurred during the Miocene period.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Blake V. Dickson, Jennifer A. Clack, Timothy R. Smithson, Stephanie E. Pierce
Summary: The analysis of humeri shows that changes in shape are driven by both ecology and phylogeny, with functional trade-offs related to locomotor performance. The evolution of terrestrial locomotion in tetrapods involved the acquisition of limb-based locomotion, leading to the diversification of terrestrial tetrapods and establishment of modern ecological niches. Stem tetrapods may have used transitional gaits during the initial stages of land exploration, stabilized by opposing selective pressures of amphibious habits.
Article
Biochemistry & Molecular Biology
Peiwen Xiong, C. Darrin Hulsey, Carmelo Fruciano, Wai Y. Wong, Alexander Nater, Andreas F. Kautt, Oleg Simakov, Martin Pippel, Shigehiro Kuraku, Axel Meyer, Paolo Franchini
Summary: This study compared two closely related Neotropical cichlid fish lineages using 40 resequenced genomes and two de novo assembled genomes. Despite inhabiting similar ecological environments, the evolutionary outcomes of the two lineages were markedly different.
Article
Biology
Karan J. Odom, Marcelo Araya-Salas, Janelle L. Morano, Russell A. Ligon, Gavin M. Leighton, Conor C. Taff, Anastasia H. Dalziell, Alexis C. Billings, Ryan R. Germain, Michael Pardo, Luciana Guimaraes de Andrade, Daniela Hedwig, Sara C. Keen, Yu Shiu, Russell A. Charif, Michael S. Webster, Aaron N. Rice
Summary: Animals produce a wide variety of sounds with highly variable acoustic structures, and phylogenetic comparative analyses can help understand the causes and consequences of this variation. Acoustic and evolutionary analyses are becoming increasingly sophisticated, making it challenging to choose appropriate methods. By providing a roadmap for quantifying and comparing sound in a phylogenetic context, researchers can address some of the challenges in this field.
BIOLOGICAL REVIEWS
(2021)
Article
Parasitology
Adriana M. Santodomingo, Richard S. Thomas, Julian F. Quintero-Galvis, Diana M. Echeverry-Berrio, Maria Carolina Silva-de la Fuente, Lucila Moreno-Salas, Sebastian Munoz-Leal
Summary: New bacteria and protozoa were discovered in rodents and marsupials in northern Chile, expanding the range of tick-borne apicomplexans in South America. The study also reported for the first time the presence of the B. microti group infecting rodents in the region. Phylogenetic analysis provided insights into the relatedness of these organisms with those found in other regions.
PARASITOLOGY RESEARCH
(2022)
Article
Multidisciplinary Sciences
Wai Lok So, Wenyan Nong, Yichun Xie, Tobias Baril, Hai-yao Ma, Zhe Qu, Jasmine Haimovitz, Thomas Swale, Juan Diego Gaitan-Espitia, Kwok Fai Lau, Stephen S. Tobe, William G. Bendena, Zhen-peng Kai, Alexander Hayward, Jerome H. L. Hui
Summary: Myriapods, specifically centipedes and millipedes, have undergone rapid genome evolution shaped by ecological pressures. The differences in their genomic pathways are a result of their divergence from the myriapod ancestor.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Cheng Wenda, Juan Diego Gaitan-Espitia, Jaiber J. Solano-Iguaran, Akihiro Nakamura, Bartosz M. Majcher, Louise A. Ashton
Summary: Assessing the heat tolerance (CTmax) of organisms is crucial for understanding the impact of climate change on biodiversity. This study investigated how environment, evolutionary history, and their interactions influence species interactions in tropical rainforests under climate change. Findings showed that phylogeny played a significant role in determining heat tolerance in herbivore-parasitoid communities. The study also highlighted the vulnerability of parasitoids and herbivore control in tropical rainforests, particularly in the canopy.
Article
Marine & Freshwater Biology
Xin Dang, Qi Huang, Yuan-Qiu He, Juan Diego Gaitan-Espitia, Tong Zhang, Vengatesen Thiyagarajan
Summary: Ocean acidification can have significant effects on the phenotypic characteristics of marine organisms, both in terms of intrinsic traits and by disrupting their associated microbiomes. This study investigates the extent to which the interaction between these phenotypic changes can influence resilience to acidification, using edible oysters as a model. The researchers find that different oyster species show species-specific responses to acidification, with the coastal species exhibiting higher stress and decreased survival compared to the estuarine species. The study highlights the importance of genetic background and local adaptation in determining the response to acidification and provides insights into host-microbiota-environment interactions in future coastal acidification.
AQUATIC TOXICOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sarah A. Breedon, Anchal Varma, Julian F. Quintero-Galvis, Juan Diego Gaitan-Espitia, Carlos Mejias, Roberto F. Nespolo, Kenneth B. Storey
Summary: The marsupial Monito del monte uses torpor to save energy and survive in cold and unpredictable environments. A study found that 14 microRNAs in the heart of Monito del monte showed significant differential expression during torpor. These differentially expressed microRNAs are predicted to regulate pathways related to cardiac function and tissue protection during torpor.
Article
Limnology
Jane C. Y. Wong, John A. Raven, Montserrat Aldunate, Sebastian Silva, Juan Diego Gaitan-Espitia, Cristian A. Vargas, Osvaldo Ulloa, Peter von Dassow
Summary: Phytoplankton play a crucial role in marine biogeochemistry and ecosystems, but their response to deoxygenation is not well-studied. A review of available information on phytoplankton in oxygen minimum zones (OMZs) reveals that surface phytoplankton disappear and are replaced by unique cyanobacteria lineages below the oxycline. Several factors, including top-down grazing, respiratory demand, and irradiance, cannot fully explain this vertical structure, suggesting a potential dependence on O2-dependent pathways.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Biotechnology & Applied Microbiology
Pamela A. Fernandez, Barbara Labbe, Juan D. Gaitan-Espitia, Catriona L. Hurd, Ellie R. Paine, Anusuya Willis, Craig Sanderson, Alejandro H. Buschmann
Summary: The distribution and productivity of seaweeds are influenced by changes in temperature and inorganic nitrogen availability. The effect of the nitrate: ammonium ratio on physiological traits and gametophyte development of Macrocystis was investigated, showing that NH4+ led to negative NO3- uptake rates and reduced growth rates. Different developmental stages and physiological traits may have varying thermal tolerance windows.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2023)
Article
Limnology
Alessia Carini, Juan Diego Gaitan-Espitia, Vengatesen Thiyagarajan
Summary: Microscopic biominerals play a crucial role in biomineralization in the ocean. The extracellular proteome secreted by organisms enhances the mineral properties. This research introduces a simple method for preparing microscopic biominerals while maintaining proteome completeness. Experimental results using Hong Kong oyster larval shells show that longer treatments and partial biomineral damage can increase protein diversity.
LIMNOLOGY AND OCEANOGRAPHY-METHODS
(2023)
Article
Environmental Sciences
J. M. Donelson, J. D. Gaitan-Espitia, A. J. Hobday, K. Mokany, S. C. Andrew, S. Boulter, C. N. Cook, F. Dickson, N. A. Macgregor, N. J. Mitchell, M. Pickup, R. J. Fox
Summary: In this Perspective, the authors emphasize the importance of considering phenotypic plasticity in conservation actions and propose a framework and road map for incorporating plasticity into management. They also highlight the challenges in implementing plasticity in conservation and present a common language and framework for connecting plasticity to management actions.
NATURE CLIMATE CHANGE
(2023)
Article
Agriculture, Dairy & Animal Science
Juan Carlos Narvaez-Barandica, Julian F. Quintero-Galvis, Juan Carlos Aguirre-Pabon, Lyda R. Castro, Ricardo Betancur, Arturo Acero Pizarro
Summary: This study evaluated the comparative phylogeography of marine species with different dispersal potentials across the southern Caribbean Sea, using two putative barriers: the Magdalena River plume (MRP) and the combination of absence of a rocky bottom and permanent upwelling in the La Guajira Peninsula (ARB + PUG). Samples of each species were collected from five locations, showing evidence of phylogeographic breaks caused by the MRP and ARB + PUG barriers. Three populations were identified for A. rivasi and C. pica, while N. tessellata presented one population. A. rivasi and C. pica fit the hierarchical population model and shared a similar phylogeographic history. The results demonstrate the influence of biological traits and biogeographic barriers on the phylogeographic structure of these species.
Editorial Material
Environmental Sciences
Da Huo, Juan Diego Gaitan-Espitia, John I. Spicer, Hongsheng Yang
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biodiversity Conservation
Gretta T. Pecl, Rachel Kelly, Chloe Lucas, Ingrid van Putten, Renuka Badhe, Curtis Champion, I-Ching Chen, Omar Defeo, Juan Diego Gaitan-Espitia, Birgitta Evengard, Damien A. Fordham, Fengyi Guo, Romina Henriques, Sabine Henry, Jonathan Lenoir, Henry McGhie, Tero Mustonen, Stephen Oliver, Nathalie Pettorelli, Malin L. Pinsky, Warren Potts, Julia Santana-Garcon, Warwick Sauer, Anna-Sofie Stensgaard, Morgan W. Tingley, Adriana Verges
Summary: Our understanding of climate change has grown, but its observable impacts have also increased. Both mitigation and adaptation measures have not kept pace with our knowledge. It is urgent to find more effective ways to engage people in understanding the effects of climate change.
Article
Meteorology & Atmospheric Sciences
Steve Widdicombe, Kirsten Isensee, Yuri Artioli, Juan Diego Gaitan-Espitia, Claudine Hauri, Janet A. Newton, Mark Wells, Sam Dupont
Summary: Approximately one-quarter of CO2 emitted by human activities is absorbed by the ocean annually, causing a reduction in seawater pH and changes in carbonate chemistry. While substantial progress has been made in observing the physicochemical changes, understanding the biological consequences of ocean acidification remains challenging.
Article
Environmental Sciences
Milica Stankovic, Amrit Kumar Mishra, Yusmiana P. Rahayu, Jonathan Lefcheck, Daniel Murdiyarso, Daniel A. Friess, Marko Corkalo, Teodora Vukovic, Mathew A. Vanderklift, Syed Hilal Farooq, Juan Diego Gaitan-Espitia, Anchana Prathep
Summary: Coastal blue carbon ecosystems in South and Southeast Asia have the potential to mitigate climate change, but current research lacks data, exhibits high variability, and shows spatial bias. Future research should address these challenges before implementing these ecosystems into national climate strategies.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)