Article
Plant Sciences
Vladimir L. Semerikov, Svetlana A. Semerikova, Yuliya Y. Khrunyk, Yuliya A. Putintseva
Summary: The study used genomic libraries enrichment and sequence capture method to obtain mtDNA data of the genus Abies and reconstructed the phylogenetic tree of the species. The results showed that Abies species can be divided into two sister branches, representing Eurasian and American species, with high support for most clades. Intraspecific variability was also found, which can be used for phylogeographic and population studies.
Review
Environmental Sciences
Wenpeng Li, Xinxin Li, Xi Mei, Fan Zhang, Jingping Xu, Chunru Liu, Chuanyi Wei, Qingsong Liu
Summary: This review highlights the importance of dating methodologies for Quaternary marine sediments in paleoceanography, summarizing the common methods of absolute and relative dating. It discusses applications and limitations of each dating methodology in various marine environments, as well as emerging event dating methods such as microplastics, mercury isotopes, and organic pollutant deposition. The review also touches on the future prospects for interdisciplinary methods to better understand natural geological evolution and predict future changes in earth science.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Yoav Vaknin, Ron Shaar, Oded Lipschits, Amihai Mazar, Aren M. Maeir, Yosef Garfinkel, Liora Freud, Avraham Faust, Ron E. Tappy, Igor Kreimerman, Saar Ganor, Karen Covello-Paran, Omer Sergi, Zeev Herzog, Rami Arav, Zvi Lederman, Stefan Munger, Alexander Fantalkin, Seymour Gitin, Erez Ben-Yosef
Summary: This study synchronizes historically dated chronological anchors and destruction layers and artifacts using the ancient geomagnetic field, resolving chronological debates regarding the campaigns against the kingdoms of Israel and Judah, the relationship between the two kingdoms, and their administrations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Xin Xu, Long Yu, Fan Li, Bingjun Wang, Fengxiang Liu, Daiqin Li
Summary: This study explores the species boundaries and phylogeny of Phrynarachne spiders in China, identifying six species and providing insights into their evolution and divergence times. The results show that Phrynarachne spiders in China have a monophyletic relationship and belong to the higher 'Thomisus group'. The estimated crown age of this genus in China is in the middle Miocene.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Connor M. French, Laura D. Bertola, Ana C. Carnaval, Evan P. Economo, Jamie M. Kass, David J. Lohman, Katharine A. Marske, Rudolf Meier, Isaac Overcast, Andrew J. Rominger, Phillip P. A. Staniczenko, Michael J. Hickerson
Summary: Understanding global patterns of genetic diversity is crucial for studying and preserving biodiversity. This study creates a global map of predicted insect mitochondrial genetic diversity and identifies the environmental factors associated with genetic diversity. The findings contribute to our understanding of global biodiversity patterns in the most diverse animal group and have important implications for conservation efforts.
NATURE COMMUNICATIONS
(2023)
Article
Anthropology
Eythan Levy, Eli Piasetzky, Alexander Fantalkin
Summary: Cross dating, a method used by archaeologists to date archaeological contexts of unknown age based on known contexts, lacks proper mathematical modeling and a precise methodology. This paper proposes a formal definition of cross dating, discusses its complexity and limitations, and presents practical solutions to address these limitations. A comprehensive scheme for modeling real-life cross dating applications based on the ChronoLog software is demonstrated, with a case study from Aegean Bronze Age archaeology to illustrate the concepts.
ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Yoon-ha Jang, Sae Ryun Ahn, Ji-yeon Shim, Kwang-il Lim
Summary: Mitochondria are intracellular energy generators whose dysfunction can lead to serious diseases. Understanding the molecular mechanisms underlying mitochondrial dysfunction is crucial for treating mitochondrial diseases. This review summarizes the key genetic processes, core genetic components, and genetic methods used to alleviate the adverse effects of mutations on mitochondrial physiology and functions.
Article
Biochemistry & Molecular Biology
Zhongjie Tang, Zhaolian Lu, Baizhen Chen, Weixing Zhang, Howard Y. Chang, Zheng Hu, Jin Xu
Summary: In this study, the researchers analyzed mitochondrial DNA mutations in over 30,000 human cells and found an overrepresentation of mutations in lymphocytes compared to hematopoietic progenitors and myeloid cells. They also found that mtDNA replication lags behind cell proliferation in lymphoid cells, potentially causing a genetic bottleneck. This study reveals a lymphoid-specific mtDNA genetic bottleneck, shedding light on how highly metabolically active immune cells limit their mtDNA mutation load.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Electrochemistry
Antonio Domenech-Carbo, Marianne Moedlinger, Laura Osete-Cortina, Maria Teresa Domenech-Carbo
Summary: The article describes a multiple-scan voltammetry strategy applied to a set of Bronze Age and later copper/bronze objects mainly from sites in Central Europe. This methodology allows the study of the compositional and textural properties of the patina and can discriminate samples of different provenance and manufacturing technique.
Review
Geosciences, Multidisciplinary
Xianglong Chen
Summary: Radiocarbon dating is a well-established technique in Chinese archeology, with significant achievements in measurement techniques, sample preparation, and chronological frameworks. However, China has reported fewer radiocarbon dates compared to Western countries. This paper provides an overview of the history of radiocarbon dating in China and its applications, highlighting breakthroughs in various archeological periods.
FRONTIERS IN EARTH SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Alexandra Wagner, Helena Kosnacova, Miroslav Chovanec, Dana Jurkovicova
Summary: Mitochondria play a crucial role in cellular metabolism and bioenergetics, and are involved in cancer development and treatment response. Studying the genetic and epigenetic control of mitochondria can provide insights into cancer therapy response and aid in the development of new therapeutic strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Olga De Castro, Gianluigi Bacchetta, Salvatore Brullo, Emanuele Del Guacchio, Emanuela Di Iorio, Carole Piazza, Paolo Caputo
Summary: This study investigates the morphological variability and native status of Genista etnensis, a tree endemic to Sicily, Sardinia, and Corsica. The results suggest strong isolation between populations in different biogeographical provinces and a possible origin in the middle Pleistocene.
Article
Geography, Physical
Ilaria Crotti, Amaelle Landais, Barbara Stenni, Lucie Bazin, Frederic Parrenin, Massimo Frezzotti, Florian Ritterbusch, Zheng-Tian Lu, Wei Jiang, Guo-Min Yang, Elise Fourre, Anais Orsi, Roxanne Jacob, Benedicte Minster, Frederic Prie, Giuliano Dreossi, Carlo Barbante
Summary: The TALDICE ice core drilled at Talos Dome extends the climate record for the Ross Sea Sector of the East Antarctic Ice Sheet back to approximately 343 ka, identifying warm stages of MIS 7 and 9. The new chronology TADICE-deep1 doubles the extension of the previous age scale, covering three past glacial/interglacial cycles.
QUATERNARY SCIENCE REVIEWS
(2021)
Article
Geochemistry & Geophysics
John P. Hart, J. M. Adovasio
Summary: This article presents the research findings of The Meadowcroft Rockshelter in Pennsylvania. While the rockshelter is famous for its pre-Clovis occupation, recent studies have discovered maize macrobotanical remains from higher strata dating back to the 4th century BC based on radiocarbon dating. However, accelerator mass spectrometry dating revealed that these specimens actually originated from the historical use of the rockshelter after AD 1800.
Article
Evolutionary Biology
Anastasia C. Christinaki, Spyros G. Kanellopoulos, Alexandra M. Kortsinoglou, Marios A. Andrikopoulos, Bart Theelen, Teun Boekhout, Vassili N. Kouvelis
Summary: This study investigates the evolutionary relationships among Saccharomycotina yeasts from a mitochondrial genomic perspective. The findings suggest that the diversity in mitochondrial genome size is a result of random processes such as genetic recombination and intron mobility. The study also reveals conserved syntenic units and rearrangements that correlate with major evolutionary events.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Agronomy
Nikolai Kondratev, Martin J. Middleditch, Matthew Denton-Giles, Rosie E. Bradshaw, Murray P. Cox, Paul P. Dijkwel
Summary: Ciborinia camelliae is a fungal pathogen that causes rapid browning and flower drop on ornamental plants of the genus Camellia. The proteins secreted by C. camelliae are necrogenic and proteinaceous in nature, with a functional distribution similar to other related fungi. While some of these proteins might contribute to virulence, they do not determine host specificity.
Article
Biochemistry & Molecular Biology
Monika Karmin, Rodrigo Flores, Lauri Saag, Georgi Hudjashov, Nicolas Brucato, Chelzie Crenna-Darusallam, Maximilian Larena, Phillip L. Endicott, Mattias Jakobsson, J. Stephen Lansing, Herawati Sudoyo, Matthew Leavesley, Mait Metspalu, Francois-Xavier Ricaut, Murray P. Cox
Summary: Island Southeast Asia and Oceania are regions with rich human phenotypic, linguistic, and cultural diversity. However, the genetic lineage of males in this region has remained unresolved. This study analyzed the Y chromosome sequence of over 380 men from the region and created a high-resolution phylogeny, revealing important population bursts and localized historical events. This research sheds light on the past isolation, interaction, and change in this understudied region.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Baojun Wu, Weilong Hao, Murray P. Cox
Summary: Our systematic analysis of 304 genomes from major fungal groups has identified 188 novel orthogroups associated with major evolutionary changes in fungi. These orthogroups were found to play key roles in trait innovations in extant fungi, such as cell wall formation, hyphal growth, and mating signaling. Prokaryote-derived horizontal gene transfer was also identified as a small additional source of evolutionary novelty.
Article
Ecology
Anna H. Behling, David J. Winter, Austen R. D. Ganley, Murray P. Cox
Summary: Hybridization is a common route to speciation in eukaryotes, and the success of allopolyploids and homoploid hybrids is well documented. Genome merger has a greater effect on posthybridization gene expression patterns than changes in ploidy. Differentially expressed genes in parent species preferentially switch to more similar expression in hybrids, likely due to regulatory trans-acting cross-talk within the hybrid nucleus. Gene loss or silencing is prevalent among extremely differentially expressed genes in hybrid species.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Microbiology
Mathieu Quenu, Artemis D. Treindl, Kate Lee, Daigo Takemoto, Torsten Thuenen, Samad Ashrafi, David Winter, Austen R. D. Ganley, Adrian Leuchtmann, Carolyn A. Young, Murray P. Cox
Summary: Genome rearrangements are common in filamentous fungi, but little is known about their evolution. In this study, we compared 15 complete genomes of the filamentous fungus genus Epichloe and found that the distinction between gene-rich and repeat-rich regions observed in isolated species is widespread across the Epichloe genus. Despite having the same number of nuclear chromosomes, the genomes of Epichloe species show low synteny and substantial rearrangement of gene content. These rearrangements are lineage-dependent and occur over short evolutionary distances with long periods of structural stability.
Article
Multidisciplinary Sciences
Nicolas Brucato, Mathilde Andre, Georgi Hudjashov, Mayukh Mondal, Murray P. Cox, Matthew Leavesley, Francois-Xavier Ricaut
Summary: A study found that there was a strong selection pattern in the genomes of the earliest settlers in Oceania, corresponding to a specific period between 52,000 and 54,000 years ago. This suggests that pathogens and plant resources exerted strong selective pressures on the genomes of the first settlers.
Article
Biology
Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw, Carl H. Mesarich
Summary: Apple scab, caused by biotrophic fungus Venturia inaequalis, is a major economic disease of apples globally. This study analyzed the transcriptome of V. inaequalis during colonization of apple, revealing five temporal waves of gene expression with most effector candidates peaking in mid-late infection. Structural predictions showed similarity between V. inaequalis effectors and avirulence proteins from other plant-pathogenic fungi, supporting the hypothesis of evolution from ancestral genes with sequence-unrelated but structurally similar proteins.
Article
Microbiology
Murray P. Cox, Yanan Guo, David J. Winter, Diya Sen, Nicholas C. Cauldron, Jason Shiller, Ellie L. Bradley, Austen R. Ganley, Monica L. Gerth, Randy F. Lacey, Rebecca L. McDougal, Preeti Panda, Nari M. Williams, Niklaus J. Grunwald, Carl H. Mesarich, Rosie E. Bradshaw
Summary: Understanding how Phytophthora pathogens infect their hosts and cause disease is crucial for the development of effective treatments. In this study, the P. agathidicida genome was successfully assembled into chromosomes, revealing that candidate effector genes are predominantly found in gene-poor, repeat-rich regions and have undergone transposon-mediated recombination. Further analysis of this complete genome assembly will aid in the development of new methods for disease control and provide insights into the evolution and adaptation of Phytophthora pathogens.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
David J. Winter, Bevan S. Weir, Travis Glare, Johanna Rhodes, John Perrott, Matthew C. Fisher, Jason E. Stajich, Andrew Digby, Peter K. Dearden, Murray P. Cox
Summary: Kakapo, a critically endangered species of parrots, experienced a devastating outbreak of aspergillosis in 2019, resulting in a significant decrease in population. Genetic analysis revealed that the outbreak was caused by a single strain of aspergillus, which was present on two islands but only caused disease on one. This study provides valuable insights into the outbreak and potential strategies for future management.
Article
Genetics & Heredity
Davide M. Vespasiani, Guy S. Jacobs, Laura E. Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, Francois-Xavier Ricaut, Murray P. Cox, Irene Gallego Romero
Summary: Modern humans have admixed with multiple archaic hominins, and Papuans owe up to 5% of their genome to Denisovans. Investigation of Papuan genomes reveals that Denisovan alleles strongly affect immune-related cells and potentially alter the binding affinity of multiple transcription factors to DNA, impacting phenotypic traits.
Article
Psychology, Biological
Aisling Rayne, Hitaua Arahanga-Doyle, Bethany Cox, Murray P. Cox, Catherine M. Febria, Stephanie J. Galla, Shaun C. Hendy, Kirsten Locke, Anna Matheson, Aleksandra Pawlik, Tom Roa, Emma L. Sharp, Leilani A. Walker, Krushil Watene, Priscilla M. Wehi, Tammy E. Steeves
Summary: The current science system is unfair in its memberships, outputs, and outcomes. We advocate for collective action to establish a more just science system that shows care for all participants. To achieve this, we urge the science community to harness complexity processes with intention.
NATURE HUMAN BEHAVIOUR
(2023)
Article
Ecology
Joseph Guhlin, Marissa F. Le Lec, Jana Wold, Emily Koot, David Winter, Patrick J. Biggs, Stephanie J. Galla, Lara Urban, Yasmin Foster, Murray P. Cox, Andrew Digby, Lydia R. Uddstrom, Daryl Eason, Deidre Vercoe, Tane Davis, Jason T. Howard, Erich D. Jarvis, Fiona E. Robertson, Bruce C. Robertson, Neil J. Gemmell, Tammy E. Steeves, Anna W. Santure, Peter K. Dearden
Summary: The study investigated the genetic variation and phenotypic influences in the critically endangered kakapo parrot using whole-genome sequence data and phenotype data. Associations were found between genic regions and traits such as growth and disease susceptibility. The study also showed that active management has maintained genetic diversity and evolutionary potential in the species. The findings provide insights for future conservation management decisions for the kakapo.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Ecology
Priscilla M. Wehi, Murray P. Cox, Hemi Whaanga, Tom Roa
Summary: Cultural wellbeing and resilience are crucial in Indigenous communities affected by colonization. Large gatherings and food systems play a significant role in expressing customary philosophies and practices, as well as bringing families together. The two Indigenous Maori communities in New Zealand demonstrate collective resilience and commitment to cultural vitality in their food systems.
ECOLOGY AND SOCIETY
(2023)
Article
Anthropology
J. Stephen Lansing, Guy S. Jacobs, Sean S. Downey, Peter K. Norquest, Murray P. Cox, Steven L. Kuhn, John H. Miller, Safarina G. Malik, Herawati Sudoyo, Pradiptajati Kusuma
Summary: A genetic analysis indicates that the Punan Batu group in Borneo, who identify themselves as still-nomadic hunter-gatherers, are unlikely to have descended from neighboring agriculturalists. They also preserve a unique song language and utilize message sticks to maintain contact, cooperate, and share resources.
EVOLUTIONARY HUMAN SCIENCES
(2022)
Article
Mycology
Torsten Thuenen, Yvonne Becker, Murray P. Cox, Samad Ashrafi
Summary: In this study, a new haploid and stroma forming species, Epichloe scottii sp. nov., isolated from Melica uniflora in Germany, is described. Phylogenetic analysis based on the tubB and tefA genes supports that E. scottii is a distinct species and the unknown ancestor of hybrid E. disjuncta. The distribution analysis shows high infection rate at the initial sampling site with only two more spots showing low infection rates. Genetic variations in key genes suggest that E. scottii sp. nov. may not be capable of producing major alkaloids.