Article
Biochemistry & Molecular Biology
Kara Ryan, Ryan Greenway, Jake Landers, Lenin Arias-Rodriguez, Michael Tobler, Joanna L. Kelley
Summary: Hydrogen sulfide is a toxic gas that disrupts biological processes, yet fish in the Poecilia mexicana species complex have evolved sulfide tolerance multiple times. This study investigates whether the repeated evolution of tolerance is due to similar genomic changes, finding evidence of both convergence and divergence in gene variation associated with sulfide processes and toxicity.
Article
Biochemistry & Molecular Biology
Nanako Yano, Toshifumi Minamoto, Hirosi Yamaguchi, Toshiyuki Goto, Takahito Nishikata
Summary: By studying the expression patterns of Ciona globin genes, it was found that two genes are similar to vertebrate hemoglobin-alpha and -beta, and are predominantly expressed in specific organs and induced under hypoxia. However, there was no robust similarity between the other Ciona globins and vertebrate globins. These results suggest that there is some physicochemical and physiological similarity between Ciona globins and vertebrate globins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Jory Thiel, Muzaffar A. Khan, Roel M. Wouters, Richard J. Harris, Nicholas R. Casewell, Bryan G. Fry, R. Manjunatha Kini, Stephen P. Mackessy, Freek J. Vonk, Wolfgang Wuster, Michael K. Richardson
Summary: Convergence is the phenomenon where similar phenotypes evolve independently in different lineages. Resistance to toxins in animals is an example of convergence, where molecular adaptations have evolved to counteract the harmful effects of toxins. However, resistance adaptations may carry fitness costs if they disrupt the normal physiology of the resistant animal.
BIOLOGICAL REVIEWS
(2022)
Article
Ecology
Qing He, Shang Wang, Kai Feng, Sean T. Michaletz, Weiguo Hou, Wenhui Zhang, Fangru Li, Yidi Zhang, Danrui Wang, Xi Peng, Xingsheng Yang, Ye Deng
Summary: This study investigated the ecological and evolutionary characteristics of microbial communities in hot springs with a broad temperature range. It found that there are two types of species, thermal-sensitive and thermal-resistant, with different ecological and evolutionary roles. Thermal-sensitive species have high fitness but low abundance, while thermal-resistant species have wide niches but poor local performance. However, these two types of species interact and co-evolve, maintaining a constant exclusion probability of thermal-resistant species.
Article
Ecology
Bri L. Ports, Michael Jensen-Seaman
Summary: This study used a genome-wide approach to investigate protein evolution in 21 primate species and found contrasting patterns between male and female reproductive tissues. In species with high levels of sperm competition, testes-specific proteins showed strong conservation, while female reproductive proteins exhibited accelerated evolution. Additionally, accelerated protein evolution was observed in lymphoid tissue, suggesting a potential influence of sexual selection on adaptive immune functions.
Article
Biology
Stefano G. Giulieri, Romain Guerillot, Sebastian Duchene, Abderrahman Hachani, Diane Daniel, Torsten Seemann, Joshua S. Davis, Steven Y. C. Tong, Bernadette C. Young, Daniel J. Wilson, Timothy P. Stinear, Benjamin P. Howden
Summary: This study provides a comprehensive analysis of the genetic variations and evolutionary patterns of Staphylococcus aureus during severe infections. The findings reveal distinct evolutionary signatures and convergent mutations in genes related to antibiotic response and pathogenesis, highlighting the clinical significance of these adaptations. Non-canonical loci associated with adaptation were also identified. These results contribute to a better understanding of the molecular changes when S. aureus transitions from colonization to severe infection and may have implications for predicting clinical outcomes and developing new treatment and prevention strategies.
Article
Ecology
Ryan Hill
Summary: This study examined convergent evolution in flight-related morphology among eight mimicry complexes of 51 butterfly species from Ecuador. Results showed significant morphological differences between mimicry complexes, divided into three clusters. Flight-related morphology adds complexity to predator-prey signals and limits the evolution of color patterns.
Article
Genetics & Heredity
Mariana Pejo, Ivanna H. Tomasco
Summary: The convergent evolution of subterranean rodents is a valuable model for studying natural selection and genetic adaptations. Different approaches have identified three sites with evidence of positive selection in underground lineages, especially in the basal branch leading to the Octodontidae family and the branch leading to the coruro, suggesting adaptive changes in response to underground life. Additionally, there is evidence of convergence with another underground rodent that cannot be identified using traditional methods.
Article
Agriculture, Multidisciplinary
Umesh Patil, Krisana Nilsuwan, Natchaphol Buamard, Bin Zhang, Soottawat Benjakul
Summary: The study extracted crude hemeprotein extract (FDCHPE) from Asian seabass gills using ultrasonication, which showed potential for treating iron-deficient anemia. Ultrasonication increased extraction yields and iron contents, affected protein structure, and influenced volatile compounds.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Review
Food Science & Technology
Avtar Singh, Ajay Mittal, Soottawat Benjakul
Summary: Fish is rich in proteins and lipids, and its color is influenced by pigments such as myoglobin and astaxanthin. Microbial spoilage and chemical changes can lead to discoloration of meat. Discoloration is affected by various factors like chemical composition, handling, storage, and processing, and methods like vacuum packaging, low-temperature storage, and additives are used to tackle it.
COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY
(2022)
Article
Chemistry, Inorganic & Nuclear
Juan Cruz Palermo, Melisa Carllinni Colombo, Jonathan A. A. Semelak, Magali F. Scocozza, Fernando M. M. Boubeta, Daniel H. H. Murgida, Dariio A. Estrin, Sara E. E. Bari
Summary: This study investigated the mechanism of metal centered reduction of metmyoglobin by sulfide species under an argon atmosphere. The formation of MbFe(II) at varying ratios of excess sulfide indicated an autocatalytic reaction mechanism. The reaction rate increased at higher alkaline pHs, suggesting HS- as the relevant reactive species for the reduction. The proposed reaction mechanism involves the formation of sulfanyl radical, disulfanuidyl/disulfanudi-idyl radical anions and disulfide, and the autocatalysis is attributed to the behavior of HSS- as a fast reductant.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Analytical
Waka Sakamoto, Nanako Azegami, Tsuyoshi Konuma, Satoko Akashi
Summary: This study improved the live single-cell MS method and applied it successfully to observe hemoglobin directly sampled from human erythrocytes. By optimizing experimental methods and conditions, native mass spectra of hemoglobin were obtained using only a single erythrocyte, marking the first report of native MS for endogenous proteins using a single intact human cell.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Fanny E. Hartmann, Tiziana Vonlanthen, Nikhil Kumar Singh, Megan C. McDonald, Andrew Milgate, Daniel Croll
Summary: Convergent evolution was observed in pesticide resistance adaptation of the fungal pathogen Zymoseptoria tritici, with some loci showing convergent changes across populations while others displaying more population-specific allele frequency changes. Genome-wide association studies revealed unknown factors in azole resistance and showed that half of the known resistance loci overlapped with selective sweep regions, indicating the major selective pressure of fungicide application on the pathogen. Genomic analyses highlighted the contribution of both de novo mutations and gene flow to convergent pesticide adaptation.
Article
Biology
Manman Li, Xinmei Li, Zhipei Wu, Guanghui Zhang, Nini Wang, Mingle Dou, Shanlin Liu, Chentao Yang, Guanliang Meng, Hailu Sun, Christina Hvilsom, Guoxiang Xie, Yang Li, Zhuo hui Li, Wei Wang, Yu Jiang, Rasmus Heller, Yu Wang
Summary: This study compared the genomes of muskox and reindeer, and identified common genetic variations related to thermogenesis and circadian rhythm in the Arctic adaptation. It was also found that muskox and reindeer may enhance brown adipose tissue thermogenesis by modulating mitochondrion, lipid metabolism, and angiogenesis pathways. Additionally, an amino acid substitution in the angiogenesis-related gene HIF2A was found to increase angiogenesis of brown adipose tissue. In conclusion, this work provides new insights into the molecular mechanisms involved in Arctic adaptation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Kazumi Sakai, Hiroki Ikeuchi, Chihiro Fujiyabu, Yasushi Imamoto, Takahiro Yamashita
Summary: Opsins are universal photoreceptive proteins in animals that play a role in regulating cyclic nucleotide signaling. Different types of opsins in different animals form different active states during photoconversion, and the position of the negatively charged counterion varies. Through analyzing a distinct group of opsins, researchers found that the counterion position change is related to the efficiency of signaling. This study provides insights into the evolutionary process of opsins and their signaling efficiency.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Ecology
Joanna L. Kelley, Thomas Desvignes, Kerry L. McGowan, Marcos Perez, Lenin Arias Rodriguez, Anthony P. Brown, Zach Culumber, Michael Tobler
Summary: The study identified differentially expressed miRNAs in Poecilia mexicana populations adapted to contrasting habitats, suggesting their involvement in H2S adaptation by regulating genes related to sulphide detoxification and mitochondrial function. MiRNAs play a critical role in promoting necessary functions for survival and reducing functions affected by H2S in natural populations.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Rishi De-Kayne, David Frei, Ryan Greenway, Sofia L. Mendes, Cas Retel, Philine G. D. Feulner
Summary: Technological advances in DNA sequencing have enabled the production and curation of large genomic data sets in nonmodel species, but also present challenges in combining data from different sequencing platforms. Combining data from various platforms may introduce potential biases and errors in base calling, highlighting the importance of caution and proper solutions when analyzing such data. Archiving tissue samples and associated sequences is essential for reproducibility and reusability of sequencing data in the face of evolving sequencing platform technology.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Ecology
Marvin Moosmann, Maria Cuenca-Cambronero, Stephen De Lisle, Ryan Greenway, Cameron M. Hudson, Moritz Luerig, Blake Matthews
Summary: The trophic structure of food webs is determined by trophic positions of species and individuals, which can evolve via natural selection. Understanding the temporal dynamics of food web structure is crucial for energy and nutrient fluxes. Evolution of trophic positions is influenced by environmental and genetic factors, and can be a target of selection in heterogeneous fitness landscapes along food chains. Recognizing trophic position as an evolving trait that depends on food web context provides a valuable link between behavioral foraging theory and food web dynamics.
Article
Biochemistry & Molecular Biology
John L. Coffin, Joanna L. Kelley, Punidan D. Jeyasingh, Michael Tobler
Summary: This study reveals the impact of environmental pollution on the adaptability of fish and identifies the mechanisms that enable mosquitofish to survive in heavy metal-contaminated environments, using integrated ionomic and transcriptomic data.
Article
Biochemistry & Molecular Biology
Gregory L. Owens, Thor Veen, Dylan R. Moxley, Lenin Arias-Rodriguez, Michael Tobler, Diana J. Rennison
Summary: Visual sensitivity and body pigmentation in Poecilia mexicana populations have shown significant parallel shifts towards greater medium-wavelength sensitivity and reflectance in sulphidic habitats, indicating the impact of environment on these traits. The changes may be attributed to differences in water's spectral properties and correlated ecological changes, showcasing the role of both natural and sexual selection in shaping these traits.
Review
Ecology
Maria Cuenca-Cambronero, Colin J. Courtney-Mustaphi, Ryan Greenway, Oliver Heiri, Cameron M. Hudson, Leighton King, Kimberley D. Lemmen, Marvin Moosmann, Moritz Muschick, Nare Ngoepe, Ole Seehausen, Blake Matthews
Summary: The field of paleolimnology has made significant progress in reconstructing past environmental conditions of aquatic ecosystems based on sediment records. Advances in molecular technologies have further enhanced the understanding of evolutionary processes and species diversification over long timescales. Integrative use of paleolimnological, paleogenetic, and molecular approaches provides important insights into ecological and evolutionary responses of species and communities to environmental change.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Scott Hotaling, Thomas Desvignes, John S. Sproul, Luana S. F. Lins, Joanna L. Kelley
Summary: This study utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, and compared it to other Antarctic fishes. The study revealed unique evolution and adaptation features in O. amberensis and highlighted the importance of long-read sequencing in understanding genome evolution.
Article
Biochemistry & Molecular Biology
Irune Ruiz-Gartzia, Esther Lizano, Tomas Marques-Bonet, Joanna L. Kelley
Summary: Wet specimens from museum collections can serve as a new source of DNA for scientific studies, but the overall condition of the specimens is crucial for obtaining high-quality genomic DNA.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Evolutionary Biology
Ellie E. Armstrong, Blair W. Perry, Yongqing Huang, Kiran Garimella, Heiko T. Jansen, Charles T. Robbins, Nathan R. Tucker, Joanna L. Kelley
Summary: This study reports a chromosome-level assembly of a male North American brown bear, which has a highly contiguous genome and supports the currently proposed species tree for Ursidae. The research provides support for future studies on the evolutionary history of the bear family and the physiological mechanisms behind hibernation, with broad medical implications.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Richard J. Wang, Yadira Pena-Garcia, Madeleine G. Bibby, Muthuswamy Raveendran, R. Alan Harris, Heiko T. Jansen, Charles T. Robbins, Jeffrey Rogers, Joanna L. Kelley, Matthew W. Hahn
Summary: This study examines the per-generation mutation rate in a brown bear pedigree and finds that both male bias and per-generation mutation rates are similar to that of non-hibernating species, contradicting previous theories. These findings provide new evidence for the determinants of mutation rates and mutation biases.
GENOME BIOLOGY AND EVOLUTION
(2022)
Review
Genetics & Heredity
David Juan, Gabriel Santpere, Joanna L. Kelley, Omar E. Cornejo, Tomas Marques-Bonet
Summary: Primate genomics is crucial for understanding human evolution and disease. Currently, there is limited data available on genetic diversity and functional genomics of primate species. Efforts are being made to characterize primate genomes, genetic variation, and functional landscapes. These data sets will provide insights into the genetics of primate traits and human diseases. This review discusses existing genome assemblies, genetic variation, and challenges in sample acquisition. It also explores how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will enhance our understanding of primate biology.
NATURE REVIEWS GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Kara Ryan, Ryan Greenway, Jake Landers, Lenin Arias-Rodriguez, Michael Tobler, Joanna L. Kelley
Summary: Hydrogen sulfide is a toxic gas that disrupts biological processes, yet fish in the Poecilia mexicana species complex have evolved sulfide tolerance multiple times. This study investigates whether the repeated evolution of tolerance is due to similar genomic changes, finding evidence of both convergence and divergence in gene variation associated with sulfide processes and toxicity.
Article
Zoology
Maura Palacios, Alfonso A. Gonzalez-Diaz, Lenin Arias Rodriguez, Mariana Mateos, Rocio Rodiles-Hernandez, Michael Tobler, Gary Voelker
Summary: This study investigates the genetic divergence and phylogenetic relationships of freshwater fish species in the shortfin group of subgenus Mollienesia in Mexico. The results show that the diversity of Mexican species can be attributed to multiple independent invasions from Middle America. Species north of the Trans-Mexican Volcanic Belt exhibit weak phylogenetic structure, while species south of the belt exhibit strong phylogenetic structure.
NEOTROPICAL ICHTHYOLOGY
(2023)
