Article
Plant Sciences
Stephen A. A. Smith, Nathanael Walker-Hale, Charles Tomomi Parins-Fukuchi
Summary: Heterogeneity in composition has been observed in both nucleotide and amino acid datasets of plants. Shifts in composition occur more frequently in nucleotides and are associated with certain plant clades. Although genes in these clades do not share the same composition, they tend to shift in the same direction. Further investigation is needed to understand the underlying biological processes.
Article
Biochemistry & Molecular Biology
Danyan Su, Lingxiao Yang, Xuan Shi, Xiaoya Ma, Xiaofan Zhou, S. Blair Hedges, Bojian Zhong
Summary: The study resolves the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. It estimates that land plants originated in the Precambrian, much older than widely recognized. The research emphasizes the important contribution of molecular data in the face of contentious fossil evidence and the critical scrutiny required for fossil calibrations in estimating the timescale of plant evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biodiversity Conservation
Guo-Qing Liu, Lian Lian, Wei Wang
Summary: Phylogenetics has become a powerful tool in biology, particularly in understanding the evolutionary relationships of land plants. Progress has been made in large-scale phylogenetic reconstructions of land plants, with well-built frameworks at the order and familial levels. Deep-level relationships have also been resolved using phylogenomic analyses. Future directions include constructing phylogenies at the genus and species levels, updating classification systems, integrating fossils into phylogenies, using phylogenomic data for resolving complex relationships, and building large trees using the supermatrix method.
Article
Multidisciplinary Sciences
Kevin R. Amses, D. Rabern Simmons, Joyce E. Longcore, Stephen J. Mondo, Kensuke Seto, Gustavo H. Jeronimo, Anne E. Bonds, C. Alisha Quandt, William J. Davis, Ying Chang, Brian A. Federici, Alan Kuo, Kurt LaButti, Jasmyn Pangilinan, William Andreopoulos, Andrew Tritt, Robert Riley, Hope Hundley, Jenifer Johnson, Anna Lipzen, Kerrie Barry, B. Franz Lang, Christina A. Cuomo, Nicolas E. Buchler, Igor V. Grigoriev, Joseph W. Spatafora, Jason E. Stajich, Timothy Y. James
Summary: By analyzing the genomes of flagellated fungi, we identified major evolutionary trends in non-Dikarya fungi. Our study revealed five lineages of flagellated fungi and found that some of these lineages have diploid-dominant life cycles. Additionally, we observed the loss of ancestral traits shared with animals across these fungi lineages. These findings caution against assuming that traits observed in Dikarya are representative of other fungal lineages.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Deqiang Ai, Lingfei Peng, Daozheng Qin, Yalin Zhang
Summary: This study sequenced the complete mitogenomes of three Flatidae members and discovered compositional heterogeneity and variable evolutionary rates among the mitogenomes. Phylogenetic analysis revealed the monophyly of Fulgoroidea and the application of a heterogeneous mixture model for the first time. The study provides a methodological reference for future phylogenetic research on Fulgoroidea based on a large sample size.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Plant Sciences
James W. Clark
Summary: Plant evolution has led to increased complexity through major innovations in vegetative and reproductive traits. Genome evolution has played a crucial role, with instances of gene and whole-genome duplication, horizontal gene transfer, and gene loss shaping plant diversity. The coevolution of plant genomes and phenotypes at a macroevolutionary scale has been observed during periods of dynamic genome evolution. While the role of gene duplication has been extensively studied, the association between gene loss and plant phenotypic diversity deserves more attention, especially considering reductive evolution in multiple plant lineages.
Article
Environmental Sciences
Quim Zaldo-Aubanell, Isabel Serra, Albert Bach, Pablo Knobel, Ferran Campillo i Lopez, Jordina Belmonte, Pepus Daunis-I-Estadella, Roser Maneja
Summary: This study investigated the independent effects of eight LULC categories on three common health conditions and found that each LULC category has a distinctive impact on health conditions, which is clearly modified by covariates. The compositional approach provides plausible results supported by existing literature, emphasizing the importance of environmental heterogeneity in health studies.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Ecology
Jingyi Yang, Xiangyu Luo, Siran Lu, Yongchuan Yang, Jun Yang
Summary: The heterogeneity of the urban matrix significantly affects the species richness of woody plants in remnant forest patches, particularly when the urbanization level is high. Compositional heterogeneity of the urban matrix is positively correlated with the species richness of tree sapling/seedlings, while it is significantly associated with the species richness of shrubs when the change rate of urbanization level is low. Configurational heterogeneity of the urban matrix can enhance the correlation between patch attributes and the species richness of tree sapling/seedlings and shrubs.
Article
Environmental Sciences
Marina Mistretta, Teresa Maria Gulotta, Paola Caputo, Maurizio Cellura
Summary: This study evaluates the energy and environmental performances of electricity generated from Italian anaerobic digestion coupled with combined heat and power plants. It finds that small and medium plants mainly fed by organic by-products have the lowest impacts. Compared to electricity from the grid, biogas electricity has the lowest contribution in some impact categories and largest in others. In terms of global warming potential and cumulative energy demand, the impacts of biogas electricity are about 35% and 38% of that generated by the grid.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Green & Sustainable Science & Technology
Gulizar Balcioglu, Harish K. Jeswani, Adisa Azapagic
Summary: This study evaluates the life cycle environmental impacts and costs of heat and electricity generation from poplar and Miscanthus, two potential energy crops in Turkey. The results show that poplar-based combined heat and power (CHP) combustion is the best option in terms of environmental impacts. All bioenergy plants provide significant reductions in global warming potential, fossil fuel depletion, and human toxicity. Poplar-based energy plants have better environmental and economic profiles compared to Miscanthus, except when land use change is considered.
SUSTAINABLE PRODUCTION AND CONSUMPTION
(2023)
Article
Thermodynamics
S. Guillen-Lambea, E. A. Pina, L. M. Serra, M. A. Lozano, A. Lazaro
Summary: This study evaluates the environmental impacts of two medium-sized solar ORC cogeneration plants. The findings show that the system without hybridization performs better in terms of environmental performance, and the impacts during the manufacturing phase are more significant than those during the operation phase.
APPLIED THERMAL ENGINEERING
(2022)
Article
Engineering, Environmental
Mojtaba Sardarmehni, James W. Levis, Morton A. Barlaz
Summary: This study compares the environmental impacts of using compost as a soil amendment to using it as alternative daily cover (ADC) in landfills. The results show that the ADC scenario outperforms the soil amendment scenario in terms of global warming potential, acidification, and eutrophication, while the soil amendment scenario performs better in cumulative energy demand and abiotic resource depletion potential.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Mathematics
Lijun Shang, Baoliang Liu, Kaiye Gao, Li Yang
Summary: Driven by the digital technologies, this paper proposes two random maintenance models based on usage categories to ensure the reliability of product life cycle. The first model, RFRW-H, focuses on warranty-stage reliability from the perspective of heterogeneity, while the second model, CRPRF or CRPRL, aims to ensure post-warranty-stage reliability by considering the cost rate function. The limits of cost and time measures as well as the cost rate functions are calculated for different maintenance models.
Article
Engineering, Environmental
Silvia Iodice, Elena Garbarino, Maria Cerreta, Davide Tonini
Summary: This study focuses on the socio-economic and environmental implications of Construction and Demolition Waste management in the Campania Region, Italy, investigating three scenarios: Status Quo, Linear Economy, and Best Practice. It highlights the significant potential environmental and social benefits of best practices, such as saving CO2 emissions and creating additional jobs, but also points out that economic costs may hinder their application.
Article
Evolutionary Biology
Mezzalina Vankan, Simon Y. W. Ho, David A. Duchene
Summary: Phylogenetic analyses using genomic data are powerful for reconstructing evolutionary relationships, but conflicting signals between loci can be a challenge. By identifying influential signals for species-tree estimation, researchers can make informed choices when selecting data for phylogenomics. Analysis of 30 phylogenomic data sets revealed associations between branch-length characteristics of gene trees and their distance from species trees, suggesting that loci with high root-to-tip distance variation may provide distinct signals for tree topology in phylogenomic studies.
SYSTEMATIC BIOLOGY
(2022)
Article
Plant Sciences
Chi-Chuan Chen, Jaakko Hyvonen, Harald Schneider
Summary: The fern family Polypodiaceae is one of the most species-rich families of ferns, playing a significant role in vascular epiphytic diversity in tropical regions. The study finds that some species can colonize successfully in habitats such as rivers, rocks, and land, in addition to epiphytic growth. It is suggested that the non-epiphytic habitat preferences may have evolved from the plesiomorphic habitat preference of epiphytes. Climate fluctuations and geographical changes during the Oligocene and Miocene periods provided opportunities for niche colonization.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Evolutionary Biology
Peter G. Foster, Dominik Schrempf, Gergely J. Szollosi, Tom A. Williams, Cymon J. Cox, T. Martin Embley
Summary: Long branches and compositional heterogeneity in protein sequences can pose problems in phylogenetic reconstruction. Recoding alignments can help mitigate these issues, but the effectiveness depends on the specific characteristics of the data. Exchangeability-based recoding generally improves accuracy, while Chi-squared-based recoding may decrease accuracy. However, the impact of recoding on accuracy varies when dealing with alignments that exhibit different types of compositional heterogeneity. It is important to exercise caution when interpreting trees generated from recoded amino acid data sets and consider alternative models that directly account for the patterns in the data.
SYSTEMATIC BIOLOGY
(2023)
Review
Plant Sciences
Alexander M. C. Bowles, Christopher J. Williamson, Tom A. Williams, Timothy M. Lenton, Philip C. J. Donoghue
Summary: Plant evolution has had a profound impact on the biosphere. Recent studies using comparative genomics, phylogenetics, and the fossil record have revealed the evolutionary history of important plant groups and key innovations. Molecular clock analyses suggest that these plant groups emerged at specific time periods in Earth's history.
TRENDS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Zhikun Gai, Xianghong Lin, Xianren Shan, Humberto G. Ferron, Philip C. J. Donoghue
Summary: Based on well-preserved fossils from the early Devonian of Guangxi, South China, the complete and articulated remains of Foxaspis novemura provide insights into the swimming speed and tail morphology of galeaspids, indicating disparate postcranial anatomies. These findings reject the hypothesis of a driven trend towards increasingly active food acquisition in early vertebrate evolution.
NATIONAL SCIENCE REVIEW
(2023)
Article
Biodiversity Conservation
Markus Ruhsam, Deborah Kohn, Jeannine Marquardt, Andrew R. R. Leitch, Harald Schneider, Johannes Vogel, Spencer C. H. Barrett, Philip E. E. Hulme, Jane Squirrell, Peter M. M. Hollingsworth
Summary: Hybridisation is an important force in plant evolution, but it can lead to genetic swamping and extinction. The widespread occurrence of non-native bluebells in the UK has raised concerns that the native bluebell could be at risk due to hybridisation. This study determines the taxonomic identity of non-natives and investigates the amount of hybridisation occurring in UK bluebell populations.
PLANTS PEOPLE PLANET
(2023)
Review
Biochemistry & Molecular Biology
Philip C. J. Donoghue, Chris Kay, Anja Spang, Gergely Szollosi, Anna Nenarokova, Edmund R. R. Moody, Davide Pisani, Tom A. Williams
Summary: The origin of eukaryotes is a highly debated topic in evolutionary biology, with multiple theories trying to explain the acquisition of eukaryotic characteristics. The main controversy stems from differing views on the defining characteristics of eukaryotes. By defining eukaryotes phylogenetically, we can clarify areas of agreement and test disagreements among hypotheses. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes, while others differ in the order of key evolutionary steps that cannot currently be distinguished phylogenetically.
Article
Biochemistry & Molecular Biology
Emily Carlisle, Christine M. Janis, Davide Pisani, Philip C. J. Donoghue, Daniele Silvestro
Summary: The origin of placental mammals has been a subject of debate, with molecular clock estimates suggesting an origin before the K-Pg extinction event, while the absence of definitive fossils before the boundary indicates a post-Cretaceous origin. However, a Bayesian Brownian bridge model suggests a Late Cretaceous origin for placental mammals. The findings support the hypothesis that placental mammals originated shortly before the K-Pg mass extinction.
Article
Plant Sciences
Shabir A. Rather, Josphat K. Saina, Arjun Adit, Hong-Mei Liu, Zhao-Yang Chang, Harald Schneider
Summary: This study establishes a DNA barcoding protocol for reliable species identification of the legume genus Caragana. The nuclear region internal transcribed spacer (nrITS) and the chloroplast region trnH-psbA are found to be the most suitable barcode loci for species discrimination. The study also provides insights into taxonomic issues in the Caragana opulens complex.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Editorial Material
Multidisciplinary Sciences
Zhikun Gai, Philip C. J. Donoghue
Summary: An analysis of a 458-million-year-old fossil fish sheds light on the evolution of vertebrate skull organization and provides anatomical insights into the transition from ancestral early vertebrates to jawed vertebrates.
Article
Biology
Thomas J. J. Smith, Robert S. S. Sansom, Davide Pisani, Philip C. J. Donoghue
Summary: Analyses of morphological disparity examine how phenotypic variation changes through time by incorporating living and fossil taxa. However, non-random patterns of data loss in fossil data due to taphonomic processes could distort perceptions of disparity. This study investigates the effects of random and structured data loss on measures of disparity and suggests caution in extrapolating general patterns in disparity from datasets that may only represent a subset of traits sampled.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Heather E. Grant, Andrew N. Ostrovsky, Helen L. Jenkins, Leandro M. Vieira, Dennis P. Gordon, Peter G. Foster, Olga N. Kotenko, Abigail M. Smith, Bjoern Berning, Joanne S. Porter, Javier Souto, Wayne K. Florence, Kevin J. Tilbrook, Andrea Waeschenbach
Summary: Parental care is crucial for the survival and evolutionary success of offspring in metazoan groups. This study investigated the evolution of incubation chambers in bryozoans and found that at least 10 different types of brood chambers evolved in the Cheilostomatida order. The modular nature of bryozoans likely contributed to the diverse array of incubation chambers observed.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Joao M. Brazao, Peter G. Foster, Cymon J. Cox
Summary: In this study, the computational efficiency and accuracy of five methods for estimating substitution models were tested. Data-specific models were found to perform better than empirical models, with IQ-TREE and P4 (maximum likelihood) being the most accurate at estimating data-specific models. Additionally, the use of data-specific protein models resulted in a better fit to the data and different tree topologies compared to empirical models when re-analyzing published datasets.
Correction
Biology
Humberto G. Ferron, Philip C. J. Donoghue
COMMUNICATIONS BIOLOGY
(2023)
Article
Plant Sciences
James W. Clark, Alexander J. Hetherington, Jennifer L. Morris, Silvia Pressel, Jeffrey G. Duckett, Mark N. Puttick, Harald Schneider, Paul Kenrick, Charles H. Wellman, Philip C. J. Donoghue
Summary: The diverse bodyplans in the plant kingdom were achieved through reproductive innovations, extinction of evolutionary intermediates, and lineage-specific evolution. The complexity of plant phenotypes is correlated with ploidy history, indicating the role of genome duplication in plant macroevolution. The pattern of increasing disparity in the plant kingdom mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern is also observed in animals and fungi, suggesting a general pattern for the evolution of multicellular bodyplans.