Article
Microbiology
Sviatoslav Rybnikov, Zeev Frenkel, Abraham B. Korol, Tzion Fahima
Summary: The study explores how interactions between parasites and hosts affect the host's recombination mechanisms, showing that in some cases, plastic recombination may be favored, especially in situations of strong selection intensity or high recombination rates in hosts. The prevention strategy is favored more frequently than the remediation strategy in these cases.
Article
Biochemistry & Molecular Biology
Yann Bourgeois, Peter D. Fields, Gilberto Bento, Dieter Ebert
Summary: The link between long-term host-parasite coevolution and genetic diversity plays a key role in genetic epidemiology and the evolution of resistance. Evidence for long-term balancing selection at both phenotypic and genomic levels was found in a specific host-parasite system, indicating a direct link between the host's resistance to a pathogen and the diversity of its underlying genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Abhishek Sharma, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker, Leroy Cronin
Summary: Scientists propose assembly theory (AT) as a framework that connects physics and biology. In AT, objects are redefined and measured by their possible formation histories. This theory provides a unified language for explaining selection, evolution, and novelty generation.
Article
Multidisciplinary Sciences
Abhishek Sharma, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker, Leroy Cronin
Summary: Scientists have struggled to reconcile biological evolution with the laws of physics. To understand the emergence of diverse forms without a design blueprint, a new framework called assembly theory (AT) has been proposed. AT redefines the concept of an object and incorporates selection and novelty generation into the physics of complex objects. It provides a powerful interface between physics and biology, revealing new aspects of physics at the chemical scale.
Article
Biology
Fredrik Jansson, Elliot Aguilar, Alberto Acerbi, Magnus Enquist
Summary: The field of cultural evolution aims to understand how individual-level processes of transmission and selection lead to population-wide patterns of cultural diversity and change; cultural traits bear relationships to one another that affect the transmission and selection process; introducing structure changes cultural dynamics.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Genetics & Heredity
Maridel Fredericksen, Peter S. Fields, Louis Du Pasquier, Virginie S. Ricci, Dieter Ebert
Summary: Identifying genes that confer resistance in a coevolving host-parasite system is important for understanding evolution. By comparing resistant and susceptible hosts, analyzing gene expression data, and performing genetic crosses, this study identifies eight candidate genes that may confer resistance to parasites. This research expands our understanding of resistance loci and provides candidates to be tested in future experiments.
Review
Biology
Alex Mesoudi
Summary: This article discusses two broad versions of human cultural evolution in the literature, one emphasizing cultural selection and the other biased transformation of cultural variants, pointing out that they are not mutually exclusive. Identifying cultural dynamics in real-world cultural data is challenging, but fine-grained historical analysis, experiments, and formal models offer the best way to distinguish them.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Magdalena Migalska, Karolina Przesmycka, Mohammed Alsarraf, Anna Bajer, Jolanta Behnke-Borowczyk, Maciej Grzybek, Jerzy M. Behnke, Jacek Radwan
Summary: In this study, the authors used long-term monitoring data of helminths infecting bank voles to test the predictions of negative frequency-dependent selection (NFDS) on MHC class II. They found a complex association between MHC diversity and species richness, as well as subpopulation-specific effects of certain MHC supertypes on helminths. These findings highlight the spatial and temporal complexity of MHC-parasite associations.
Article
Biochemistry & Molecular Biology
Yixin Zhao, Guang-An Lu, Hao Yang, Pei Lin, Zhongqi Liufu, Tian Tang, Jin Xu
Summary: The Red Queen hypothesis suggests that new genes must evolve continuously to adapt to changing environments, or they will be eliminated. In an experiment with two Drosophila miRNAs, it was found that their fitness contributions differed in different species, supporting the predictions of the Red Queen hypothesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Zhanshan Ma
Summary: Microbes play a significant role in reproductive health, and the exchange of microbes during sexual intercourse is a direct and important mode of transmission between men and women. Through reanalyzing microbial datasets, it was found that microbial transmission between seminal and vaginal fluids is a stochastic, passive diffusion process and the transmission probability is approximately 0.05. This transmission process may contribute to the homogeneity between semen and vaginal microbiomes, facilitating sexual reproduction.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Evolutionary Biology
Jonathan R. Goodman, Paul W. Ewald
Summary: The barrier theory is a universal evolutionary framework for understanding coevolutionary effects of conflicts of interest in natural and human systems. It suggests that exploiters capable of overcoming barriers and restraints will be favored in conflicts of interest. Barriers can temporarily halt coevolutionary arms races and occur across a spectrum of interactions in both natural and social systems.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Biology
Mohammad Salahshour
Summary: Salahshour's study demonstrates that heterogeneity can facilitate cooperation and coexistence of cooperators and defectors in different institutes by introducing participation costs as a factor to promote cooperation.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Xukang Shen, Siliang Song, Chuan Li, Jianzhi Zhang
Summary: Synonymous mutations in protein-coding genes are not neutral and often result in reduced fitness and disturbed mRNA expression levels. Non-synonymous mutations have greater fitness variations across environments, which may explain the lower substitution rates compared to synonymous mutations.
Article
Multidisciplinary Sciences
Qipian Chen, Hao Yang, Xiao Feng, Qingjian Chen, Suhua Shi, Chung- Wu, Ziwen He
Summary: There has been a large literature on adaptive DNA sequence evolution between species in the last two decades. The main evidence comes from the McDonald-Kreitman test and the phylogenetic analysis by maximum likelihood test. However, when these two tests were applied to genomic data of Drosophila and Arabidopsis, it was found that the identified genes did not overlap, possibly due to low power and high false negatives. The study also discovered that negative selection rarely remains constant in evolution, leading to the misinterpretation of variation in negative selection as a signal of positive selection.
NATIONAL SCIENCE REVIEW
(2022)
Article
Multidisciplinary Sciences
Luis Borda-de-Agua, Stephen P. Hubbell
Summary: Credible estimates indicate that many of the nearly 7000 languages in the world could become extinct this century, which would have profound cultural, socioeconomic, and political implications. Little predictive theory exists for language dynamics and richness. Research shows that many regional language abundance distributions resemble the bell-shaped distributions predicted by neutral theory in ecology, indicating a potential equilibrium or disequilibrium between origination and extinction rates of languages. However, deviations from this pattern in some regional distributions can be explained by non-neutral processes such as systematic growth in the number of speakers due to cultural factors.
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
Genetics & Heredity
Heini M. Natri, Georgi Hudjashov, Guy Jacobs, Pradiptajati Kusuma, Lauri Saag, Chelzie Crenna Darusallam, Mait Metspalu, Herawati Sudoyo, Murray P. Cox, Irene Gallego Romero, Nicholas E. Banovich
Summary: The lack of diversity in human genomics hampers our understanding of the genetic basis of complex traits and contributes to health disparities. Through studying gene regulation in the Indonesian population, we found that population-specific genetic architecture, local ancestry, and archaic introgression play a role in gene regulation variation.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Genetics & Heredity
Daniel Berry, Kate Lee, David Winter, Wade Mace, Yvonne Becker, Padmaja Nagabhyru, Artemis D. Treindl, Esteban Valverde Bogantes, Carolyn A. Young, Adrian Leuchtmann, Linda J. Johnson, Richard D. Johnson, Murray P. Cox, Christopher L. Schardl, Barry Scott
Summary: Fungi from the genus Epichloe form endobiotic infections in cool season grasses and produce host-protective natural products. During the sexual cycle, they exhibit virulent growth, enveloping and sterilizing the host inflorescence. RNAseq analysis identified a core set of differentially expressed genes associated with host suppression, digestion, adaptation, and stroma formation.
G3-GENES GENOMES GENETICS
(2022)
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
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.