Article
Plant Sciences
Zhe Hou, Ang Li
Summary: White poplar and David's aspen are important plant species with wide distribution and adaptation abilities. Genetic divergence indicates significant allopatric speciation events during the Middle Pleistocene. Climate differences and selection played important roles in the genomic divergence of these species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Blair P. Bentley, Tomas Carrasco-Valenzuela, Elisa K. S. Ramos, Harvinder Pawar, Larissa Souza Arantes, Alana Alexander, Shreya M. Banerjee, Patrick Masterson, Martin Kuhlwilm, Martin Pippel, Jacquelyn Mountcastle, Bettina Haase, Marcela Uliano-Silva, Giulio Formenti, Kerstin Howe, William Chow, Alan Tracey, Ying Sims, Sarah Pelan, Jonathan Wood, Kelsey Yetsko, Justin R. Perrault, Kelly Stewart, Scott R. Benson, Yaniv Levy, Erica V. Todd, H. Bradley Shaffer, Peter Scott, Brian T. Henen, Robert W. Murphy, David W. Mohr, Alan F. Scott, David J. Duffy, Neil J. Gemmell, Alexander Suh, Sylke Winkler, Francoise Thibaud-Nissen, Mariana F. Nery, Tomas Marques-Bonet, Agostinho Antunes, Yaron Tikochinski, Peter H. Dutton, Olivier Fedrigo, Eugene W. Myers, Erich D. Jarvis, Camila J. Mazzoni, Lisa M. Komoroske
Summary: Sea turtles are ancient marine vertebrates that have evolved from terrestrial ancestors. Their unique physiological and ecological traits and the genomic basis behind them remain largely unknown. This study generated and analyzed high-quality reference genomes for leatherback and green turtles, revealing divergent evolution in certain gene families that may be responsible for immunological and sensory adaptations. Microchromosomes were found to play a critical role in vertebrate evolutionary adaptation. Furthermore, diversity and demographic histories differed significantly between the two species, indicating concerns over the persistence of leatherback turtles under future climate scenarios.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Editorial Material
Biochemistry & Molecular Biology
Jeremy Choin, Lluis Quintana-Murci
Summary: Ancient DNA research provides insights into the demographic processes in prehistoric Europe, shedding light on past human history.
Article
Multidisciplinary Sciences
Israel Aguilar-Ordonez, Fernando Perez-Villatoro, Humberto Garcia-Ortiz, Francisco Barajas-Olmos, Judith Ballesteros-Villascan, Ram Gonzalez-Buenfil, Cristobal Fresno, Alejandro Garciarrubio, Juan Carlos Fernandez-Lopez, Hugo Tovar, Enrique Hernandez-Lemus, Lorena Orozco, Xavier Soberon, Enrique Morett
Summary: This study conducted high-coverage whole genome sequencing of 76 unrelated individuals from 27 indigenous groups in Mexico, revealing novel genetic variations associated with prevalent health issues in the Mexican population. Positive selection signals and genetic stratification analysis showed distinctive population structures among Native Mexican groups, contributing to a better understanding of their genomic diversity.
Article
Biology
Weiting Zhang, Pierluigi Scerbo, Marine Delagrange, Virginie Candat, Vanessa Mayr, Sophie Vriz, Martin Distel, Bertrand Ducos, David Bensimon
Summary: The study reveals that in Zebrafish, the dynamics of fgf8 and other gene transcripts, as well as segmentation frequency, shortening of pre-somitic mesoderm, and tail growth rate slow down with lower temperature, potentially explaining the temperature independence of somitogenesis.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemical Research Methods
Laurent Excofffier, Nina Marchi, David Alexander Marques, Remi Matthey-Doret, Alexandre Gouy, Vitor C. Sousa
Summary: fastsimcoal2 extends fastsimcoal by enabling estimation of demographic parameters under complex scenarios, with improvements such as multi-threading, handling of population inbreeding, extended input file syntax, and more efficient simulations.
Article
Biochemistry & Molecular Biology
Omar Alva, Anais Leroy, Margit Heiske, Veronica Pereda-Loth, Lenka Tisseyre, Anne Boland, Jean-Francois Deleuze, Jorge Rocha, Carina Schlebusch, Cesar Fortes-Lima, Mark Stoneking, Chantal Radimilahy, Jean-Aime Rakotoarisoa, Thierry Letellier, Denis Pierron
Summary: Madagascar, one of the last land masses to be colonized by humans, has shown genetic and linguistic evidence of a mixture between African and Asian populations in the past millennium. The admixture coincides with rapid population growth and landscape changes, as well as the extinction of endemic large-bodied vertebrates.
Article
Multidisciplinary Sciences
Steve Horvath, Ake T. Lu, Amin Haghani, Joseph A. Zoller, Caesar Z. Li, Andrea R. Lim, Robert T. Brooke, Ken Raj, Aitor Serres-Armero, Dayna L. Dreger, Andrew N. Hogan, Jocelyn Plassais, Elaine A. Ostrander
Summary: Epigenetic clocks are reliable and highly accurate biomarkers that can be applied to 93 domestic dog breeds and potentially to humans. They are used to estimate age, lifespan, and health status, contributing to research on antiaging treatments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Plant Sciences
Joao Antonio Siqueira, Willian Batista-Silva, Agustin Zsogon, Alisdair R. Fernie, Wagner L. Araujo, Adriano Nunes-Nesi
Summary: Through domestication, humans have altered the developmental and circadian clocks of plants, resulting in modern crops with increased productivity and adaptability. However, this domestication has also led to reduced genetic variability and abiotic stress tolerance. The domestication process has likely caused a significant restructuring of plant metabolic timekeeping. We highlight the importance of the contrasting timings among organs in wild relatives of crops for recognizing environmental adversities. Furthermore, we suggest that the connections established among biological clocks during plant domestication may offer a valuable source of genetic variation for improving crop resilience and yield.
TRENDS IN PLANT SCIENCE
(2023)
Article
Microbiology
Angela Ares, Sanae Sakai, Toshio Sasaki, Shigeru Shimamura, Satoshi Mitarai, Takuro Nunoura
Summary: In deep-sea hydrothermal vent environments, the metal resistance mechanisms of Nitratiruptor sp. SB155-2 (phylum Campylobacterota) to cadmium (Cd) and copper (Cu) were investigated using transcriptomics and shotgun proteomics. The study revealed differentially transcribed genes and metal-specific adaptation pathways for Cd and Cu stress in the organisms.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yalin Cheng, Matthew J. Miller, Dezhi Zhang, Ying Xiong, Yan Hao, Chenxi Jia, Tianlong Cai, Shou-Hsien Li, Ulf S. Johansson, Yang Liu, Yongbin Chang, Gang Song, Yanhua Qu, Fumin Lei
Summary: Parallel evolution is expected among closely related taxa exposed to similar selective pressures, but genetic solutions to achieve phenotypic similarities may differ. In East Asian Paridae species, high-elevation adaptation shows parallel functional response to extreme elevation relying on different genes, with no influence of heterozygosity on genetic parallelism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Environmental Sciences
Denis Vasiliev, Sarah Greenwood
Summary: Pollinator biodiversity loss is occurring at unprecedented rates globally, with sharp declines documented in the North Temperate Zone. Climate change is expected to impact pollinator biodiversity in the future, but current warming may have positive impacts on pollinators at higher latitudes. However, the lack of climate adaptation initiatives in current conservation efforts could be risky if climate change negatively impacts pollinators.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Genetics & Heredity
Yueqi Tao, Bin Chen, Ming Kang, Yongbo Liu, Jing Wang
Summary: The study on six representative species of Cycas in South China using RADseq data revealed low genetic diversity and strong genetic differentiation across species. Phylogenetic inference and genetic structure analysis showed consistent groups among the Cycas species. Significant genetic admixture was found in individuals of C. dolichophylla, indicating complex patterns of interspecific gene flow. The study also highlighted the impacts of climate fluctuations and geological activities on the population dynamics of these species in South China.
FRONTIERS IN GENETICS
(2021)
Article
Ecology
Joe C. Gunn, Leah K. Berkman, Jeff Koppelman, Andrew T. Taylor, Shannon K. Brewer, James M. Long, Lori S. Eggert
Summary: This study revealed the genetic differences and intra-specific diversity patterns between the Neosho Bass and Smallmouth Bass through population genomic analysis. The results suggest that the Neosho Bass may be locally adapted and has been influenced by both natural and anthropogenic factors.
ECOLOGY AND EVOLUTION
(2022)
Article
Environmental Sciences
Qing-Hua Wang, Ren-Xie Wu, Zhong-Lu Li, Su-Fang Niu, Yun Zhai, Min Huang, Biao Li
Summary: This study investigated the impact of Late Pleistocene-Holocene climate fluctuations on the phylogeographic structure and demographic dynamics of Decapterus maruadsi. The results showed that the population of D. maruadsi underwent a recent demographic expansion during the Late Pleistocene-Holocene. Additionally, some samples identified as D. maruadsi were actually D. russelli. These findings reveal the complex effects of climate change on the population of D. maruadsi.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Behavioral Sciences
Tyrone Lucon-Xiccato, Giulia Montalbano, Adam R. Reddon, Cristiano Bertolucci
Summary: Living in a social group may impose cognitive demands, and cognitive abilities may be positively related to the complexity of the social system. However, environmental conditions and social stability factors may influence individual cognitive performance.
Article
Biology
Giulia Montalbano, Cristiano Bertolucci, Tyrone Lucon-Xiccato
Summary: Environmental enrichment is crucial for the neural, cognitive, and behavioral development of individuals. This study on Poecilia reticulata found that guppies raised in enriched environments learned color discrimination faster than those in barren conditions, but enrichment did not affect inhibitory control and cognitive flexibility.
Article
Multidisciplinary Sciences
Ylenia D'Agostino, Elena Frigato, Teresa M. R. Noviello, Mattia Toni, Flavia Frabetti, Luisa Cigliano, Michele Ceccarelli, Paolo Sordino, Luigi Cerulo, Cristiano Bertolucci, Salvatore D'Aniello
Summary: Using CRISPR/Cas9 technology, a valuable Bdnf null mutant line was generated in zebrafish for studying the crucial role of BDNF in circadian clock regulation. The study confirmed the modulatory role of Bdnf on zebrafish circadian behavior and suggested a connection between BDNF and circadian rhythms.
Article
Multidisciplinary Sciences
Tyrone Lucon-Xiccato, Felix Loosli, Francesca Conti, Nicholas S. Foulkes, Cristiano Bertolucci
Summary: This study analysed the behaviour of medaka in anxiety-like and sociability tests and found that it showed similarities with other teleosts in some tests but also exhibited differences. A comparison with zebrafish under the same conditions revealed significant variations in behavioural responses, indicating that medaka responds differently to experimental settings compared to other fish models.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Ilenia Urso, Alberto Biscontin, Davide Corso, Cristiano Bertolucci, Chiara Romualdi, Cristiano De Pitta, Bettina Meyer, Gabriele Sales
Summary: The krill species Euphausia superba plays a critical role in the Antarctic ecosystem, but climate changes have already affected its distribution and reproductive dynamics. In this study, we identified genes involved in the krill moulting cycle, reproductive process, and sexual maturation, and discovered previously unknown differentially expressed genes related to cuticle development and energy storage. We also expanded our knowledge of the krill opsin repertoire by finding new opsin sequences. Furthermore, we created the KrillDB(2) database, which provides comprehensive information on krill genes, expression profiles, and differential expression.
SCIENTIFIC REPORTS
(2022)
Article
Behavioral Sciences
Tyrone Lucon-Xiccato, Marco Tomain, Salvatore D'Aniello, Cristiano Bertolucci
Summary: This study investigates the effects of BDNF loss on behavior using a CRISPR/Cas9 bdnf-/- zebrafish line. The results suggest that BDNF plays a role in locomotor activity, sociability, and potentially anxiety-like behavior.
BEHAVIOURAL BRAIN RESEARCH
(2023)
Article
Marine & Freshwater Biology
Annalaura Mancia, Luigi Abelli, Giorgia Palladino, Marco Candela, Tyrone Lucon-Xiccato, Cristiano Bertolucci, Maria Cristina Fossi, Matteo Baini, Cristina Panti
Summary: This study aimed to assess the combined effects of microplastics and environmental contaminants on zebrafish health and behavior. The results showed that exposure to microplastics and pollutants can have negative effects on zebrafish, with greater impacts observed from environmentally exposed microplastics.
AQUATIC TOXICOLOGY
(2023)
Article
Environmental Sciences
Giulia Caioni, Carmine Merola, Cristiano Bertolucci, Tyrone Lucon-Xiccato, Beste Basak Savasci, Mara Massimi, Martina Colasante, Giulia Fioravanti, Nunzio Antonio Cacciola, Rodolfo Ippoliti, Michele d'Angelo, Monia Perugini, Elisabetta Benedetti
Summary: This study investigates the effects of early-life exposure to Triclocarban (TCC) on eye development and visual function in zebrafish. The results show that TCC exposure disrupts retinal architecture and impairs visual perception, suggesting potential long-term effects on zebrafish visual function.
Article
Agriculture, Dairy & Animal Science
Matteo Zarantoniello, Adriana Alves de Oliveira, Tolga Sahin, Lorenzo Freddi, Matteo Torregiani, Isabella Tucciarone, Giulia Chemello, Gloriana Cardinaletti, Elia Gatto, Giuliana Parisi, Cristiano Bertolucci, Paola Riolo, Ancuta Nartea, Giorgia Gioacchini, Ike Olivotto
Summary: Modern aquaculture is transitioning towards sustainable practices and reducing water consumption. This study focuses on using spirulina-enriched black soldier fly prepupae meal (HPM) as a more sustainable aquafeed ingredient in aquaponic systems for European seabass. The results demonstrate the suitability of aquaponic systems for rearing finfish and the positive impact of spirulina-enriched HPM on fish growth, welfare, and quality. The experimental diets showed no negative effects on survival, performance, behavior, gut health, fillet quality, and even preserved the fillet from lipid oxidation. These findings support the use of sustainable ingredients in aquaponic systems for euryhaline fish rearing.
Article
Behavioral Sciences
Giulia Montalbano, Cristiano Bertolucci, Angelo Bisazza, Tyrone Lucon-Xiccato
Summary: Most studies on developmental variation in cognition have been conducted in altricial species, such as humans, where individuals are born with reduced cognitive abilities and cognitive performance increases with age. This study explores whether species with different developmental modes exhibit different patterns of cognitive development. The findings suggest that the typical cognitive progression observed in early development may not be the only trend, and a species' developmental mode could determine variation in cognition across different ages.
Article
Biochemistry & Molecular Biology
Francesco Dalla Barba, Michela Soardi, Leila Mouhib, Giovanni Risato, Eylem Emek Akyurek, Tyrone Lucon-Xiccato, Martina Scano, Alberto Benetollo, Roberta Sacchetto, Isabelle Richard, Francesco Argenton, Cristiano Bertolucci, Marcello Carotti, Dorianna Sandona
Summary: Sarcoglycanopathies, or limb girdle muscular dystrophy 3-6, are rare muscular dystrophies that cause high disability, respiratory and cardiac problems. This study generated and characterized zebrafish models of these diseases using CRISPR/Cas9 genome editing, which showed progressive disease phenotypes. These zebrafish models will enhance our understanding of the disease and assist in drug screening and development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Psychology, Biological
Santiago Pintos, Tyrone Lucon-Xiccato, Luisa Maria Vera, Cristiano Bertolucci
Summary: This study found that the behavioral stress response in zebrafish follows a daily rhythm, with a stronger response at night. This rhythmicity may be important for improving welfare in aquaculture and enhancing the reliability of behavioral research in fish models.
PHYSIOLOGY & BEHAVIOR
(2023)
Article
Biology
Tyrone Lucon-Xiccato, Giulia Montalbano, Cristiano Bertolucci
Summary: Animal species, including humans, exhibit individual variability in cognition that is difficult to explain. This study demonstrates that cognitive plasticity contributes to this variability. The results show that guppies exposed to different levels of resource predictability develop different cognitive abilities, suggesting that adaptive cognitive plasticity is a key determinant of cognitive individual differences.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Tyrone Lucon-Xiccato, Gaia De Russi, Stefano Cannicci, Elena Maggi, Cristiano Bertolucci
Summary: The natural light cycle has a significant impact on animals' cognitive systems, and the alteration caused by human activities, such as artificial light at night (ALAN), affects the cognitive functions of mammals and birds. However, the effects of ALAN on aquatic species have not been thoroughly studied. This research showed that exposure to ALAN negatively affects the cognitive abilities of zebrafish, leading to slower learning and disruption of the relationship between learning performance and behavioral traits. Additionally, ALAN increased larval activity.
Article
Environmental Sciences
Tyrone Lucon-Xiccato, Beste Basak Savasci, Carmine Merola, Elisabetta Benedetti, Giulia Caioni, Valbona Aliko, Cristiano Bertolucci, Monia Perugini
Summary: Chemicals spilled in aquatic ecosystems can interfere with cognitive abilities and brain functions controlling fitness-related behaviour. Triclo-carban (TCC), one such contaminant, disrupts hormonal activity and has effects on behaviour and cognitive abilities in zebrafish. Exposure to TCC reduces exploratory behaviour, response to stimulation, and cognitive performance, while increasing sociability in zebrafish larvae. This is accompanied by upregulation of c-fos and downregulation of bdnf in the brain, which impact neural activity and cognitive traits. These findings highlight the importance of considering the fitness consequences of non-lethal concentrations of TCC in aquatic ecosystems and their potential to affect human health.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)