Article
Genetics & Heredity
Geng Tian, Guilian Xiao, Tong Wu, Junzhi Zhou, Wenjing Xu, Yanxia Wang, Guangmin Xia, Mengcheng Wang
Summary: The diploidization of polyploid genomes is accompanied by genomic variation and synonymous codon usage bias (SCUB). SCUB alters during the formation of hexaploid wheat and contributes to epigenetic variation. DNA methylation-mediated conversion weakens following the increase of genome ploidy, coinciding with the stronger bias for certain codons in hexaploid wheat.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Mahan Ghafari, Louis du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver G. Pybus, Aris Katzourakis
Summary: High-throughput sequencing allows rapid genome sequencing during outbreaks, providing insight into pathogen evolution dynamics. Evolutionary analyses over short timescales are challenging due to the time-dependent nature of evolutionary rate estimates. The study on SARS-CoV-2 and pH1N1 influenza found that inferred evolutionary parameters decline over time, with growth rates and emergence dates stable after 4 months. Terminal branches exhibit elevated substitution rates, correlated with purifying selection generating time dependency in evolutionary parameters.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Nicola De Maio, Conor R. Walker, Yatish Turakhia, Robert Lanfear, Russell Corbett-Detig, Nick Goldman
Summary: The COVID-19 pandemic has prompted an unprecedented response from the sequencing community, leading to a study of mutation rates and selective pressures using sequence data from over 140,000 SARS-CoV-2 genomes. Two specific mutation rates, G -> U and C -> U, were found to be significantly higher than others, possibly attributed to APOBEC and ROS activity. Genomic context does have an effect on mutation rates, but its impact is limited.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Tom Carruthers, Robert W. Scotland
Summary: Research using simulation and analysis has found that when substitution rates, speciation rates, and extinction rates vary, the benefits of increased character and taxon sampling on parameter estimation accuracy are limited. Methodological assumptions are more likely to be violated, and limitations in the information content of the data become more important in complex cases.
SYSTEMATIC BIOLOGY
(2021)
Article
Ecology
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
Summary: Morphological matrices are commonly used for dating species divergence times in systematics, either by combining morphological and molecular character data from extant taxa, or by including morphological characters from extinct taxa. Our analysis of three empirical datasets showed a high correlation between divergence time estimates from molecular and discrete morphological data of extant taxa, despite a poor linear relationship between branch lengths. Averaging effects over multiple branches may explain the discrepancy, indicating that nodes with a large number of taxa benefit from this averaging. Discordance between time estimates from molecules and morphology may still occur, particularly at intermediate nodes. It is suggested that node- and tip-calibration approaches may be better suited for nodes with many taxa, emphasizing the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before conducting dating analysis using combined datasets.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Artem N. Bondaryuk, Nina V. Kulakova, Olga I. Belykh, Yurij S. Bukin
Summary: The study evaluated the temporal signal and substitution rate of different subtypes of tick-borne encephalitis virus (TBEV). The analysis showed that the TBEV Siberian subtype lacked temporal structure and could not be used for substitution rate estimation without other TBEV subtypes. The common clade of TBEV had the lowest substitution rate among tick-borne flaviviruses, and the European subtype had the lowest rate within the common clade.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Ornithology
Angel Arcones, Raquel Ponti, David R. Vieites
Summary: Research indicates that there is variation in mtDNA molecular clock substitution rates among bird lineages and markers, casting doubt on the universality of the standard molecular clock. Specific substitution rates have been provided for each mtDNA marker in avian orders sampled, serving as a valuable tool for molecular clock analysis in the absence of fossil calibrations.
Article
Multidisciplinary Sciences
Marcos Suarez-Menendez, Martine Berube, Fabricio Furni, Vania E. Rivera-Leon, Mads-Peter Heide-Jorgensen, Finn Larsen, Richard Sears, Christian Ramp, Britas Klemens Eriksson, Rampal S. Etienne, Jooke Robbins, Per J. Palsboll
Summary: Direct estimation of germline mutation rate in baleen whales using pedigrees shows higher values than phylogeny-based estimates, similar to estimates for primates and toothed whales. Our results reduce previous genetic-based estimates of preexploitation whale abundance and challenge the explanation of low cancer rates in large mammals.
Article
Entomology
Ameyra Aman-Zuki, Siti Zafirah Ghazali, Aqilah Sakinah Badrulisham, Izfa Riza Hazmi, Othman Nurul Wahida, Salmah Yaakop
Summary: Molecular clock analysis on the oil palm weevil species revealed the separation of Red Palm Weevil and Asiatic Palm Weevil as two sympatric species, with divergence times of approximately 1.926 and 4.857 million years ago, respectively. The study utilized genetic distance analysis and construction of phylogenetic trees using COI, Cytb, and their combination to support these findings.
JOURNAL OF THE ENTOMOLOGICAL RESEARCH SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Luciano Paganucci de Queiroz, Jose Floriano B. Pastore, Domingos Cardoso, Cristiane Snak, Ana Luisa de C. Lima, Edeline Gagnon, Mohammad Vatanparast, Ailsa E. Holland, Ashley N. Egan
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2015)
Article
Plant Sciences
Yi-Jun Lu, Chuan Chen, Rui-Hong Wang, Ashley N. Egan, Cheng-Xin Fu
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2015)
Article
Plant Sciences
Ashley N. Egan, Bo Pan
Article
Biochemistry & Molecular Biology
Ashley N. Egan, Mohammad Vatanparast, William Cagle
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2016)
Review
Plant Sciences
Patrush Lepcha, Ashley N. Egan, Jeff J. Doyle, N. Sathyanarayana
PLANT FOODS FOR HUMAN NUTRITION
(2017)
Article
Plant Sciences
Nasim Azani, Marielle Babineau, C. Donovan Bailey, Hannah Banks, Ariane R. Barbosa, Rafael Barbosa Pinto, James S. Boatwright, Leonardo M. Borges, Gillian K. Brown, Anne Bruneau, Elisa Candido, Domingos Cardoso, Kuo-Fang Chung, Ruth P. Clark, Adilva de S. Conceicao, Michael Crisp, Paloma Cubas, Alfonso Delgado-Salinas, Kyle G. Dexter, Jeff J. Doyle, Jerome Duminil, Ashley N. Egan, Manuel de la Estrella, Marcus J. Falcao, Dmitry A. Filatov, Ana Paula Fortuna-Perez, Renee H. Fortunato, Edeline Gagnon, Peter Gasson, Juliana Gastaldello Rando, Ana Maria Goulart de Azevedo Tozzi, Bee Gunn, David Harris, Elspeth Haston, Julie A. Hawkins, Patrick S. Herendeen, Colin E. Hughes, Joao R. V. Iganci, Firouzeh Javadi, Sheku Alfred Kanu, Shahrokh Kazempour-Osaloo, Geoffrey C. Kite, Bente B. Klitgaard, Fabio J. Kochanovski, Erik J. M. Koenen, Lynsey Kovar, Matt Lavin, Marianne le Roux, Gwilym P. Lewis, Haroldo C. de Lima, Maria Cristina Lopez-Roberts, Barbara Mackinder, Vitor Hugo Maia, Valery Malecot, Vidal F. Mansano, Brigitte Marazzi, Sawai Mattapha, Joseph T. Miller, Chika Mitsuyuki, Tania Moura, Daniel J. Murphy, Madhugiri Nageswara-Rao, Bruno Nevado, Danilo Neves, Dario I. Ojeda, R. Toby Pennington, Darirn E. Prado, Gerhard Prenner, Luciano Paganucci de Queiroz, Gustavo Ramos, Fabiana L. Ranzato Filardi, Petala G. Ribeiro, Maria de Lourdes Rico-Arce, Michael J. Sanderson, Juliana Santos-Silva, Wallace M. B. Sao-Mateus, Marcos J. S. Silva, Marcelo F. Simon, Carole Sinou, Cristiane Snak, Elvia R. de Souza, Janet Sprent, Kelly P. Steele, Julia E. Steier, Royce Steeves, Charles H. Stirton, Shuichiro Tagane, Benjamin M. Torke, Hironori Toyama, Daiane Trabuco da Cruz, Mohammad Vatanparast, Jan J. Wieringa, Michael Wink, Martin F. Wojciechowski, Tetsukazu Yahara, Tingshuang Yi, Erin Zimmerman
Article
Biotechnology & Applied Microbiology
Matthew S. Haynsen, Mohammad Vatanparast, Gouri Mahadwar, Dennis Zhu, Roy Z. Moger-Reischer, Jeff J. Doyle, Keith A. Crandall, Ashley N. Egan
Article
Plant Sciences
Mohammad Vatanparast, Adrian Powell, Jeff J. Doyle, Ashley N. Egan
APPLICATIONS IN PLANT SCIENCES
(2018)
Article
Multidisciplinary Sciences
Mohammad Vatanparast, Prateek Shetty, Ratan Chopra, Jeff J. Doyle, N. Sathyanarayana, Ashley N. Egan
SCIENTIFIC REPORTS
(2016)
Article
Multidisciplinary Sciences
Ashley N. Egan, Shanna Moore, Giulia Marina Stellari, Byoung-Cheorl Kang, Molly M. Jahn
Article
Biochemistry & Molecular Biology
Yiyong Zhao, Rong Zhang, Kai-Wen Jiang, Ji Qi, Yi Hu, Jing Guo, Renbin Zhu, Taikui Zhang, Ashley N. Egan, Ting-Shuang Yi, Chien-Hsun Huang, Hong Ma
Summary: This study provides a highly resolved phylogeny of Fabaceae, including the resolution of inter-relationships between subfamilies, estimation of early radiation events near the K/Pg boundary, and identification of numerous whole-genome duplication events. Additionally, the evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed, revealing one or two switches to rhizobial nodulation followed by multiple losses. These results lay the foundation for further evolutionary analyses across Fabaceae.
Article
Biodiversity Conservation
Ashley N. Egan
WESTERN NORTH AMERICAN NATURALIST
(2020)
Article
Plant Sciences
Anne Bruneau, Leonardo M. Borges, Robert Allkin, Ashley N. Egan, Manuel de la Estrella, Firouzeh Javadi, Bente Klitgaard, Joseph T. Miller, Daniel J. Murphy, Carole Sinou, Mohammad Vatanparast, Rong Zhang
AUSTRALIAN SYSTEMATIC BOTANY
(2019)
Article
Plant Sciences
Ashley N. Egan, Mohammad Vatanparast
AUSTRALIAN SYSTEMATIC BOTANY
(2019)
Article
Biotechnology & Applied Microbiology
N. Sathyanarayana, Ranjith Kumar Pittala, Pankaj Kumar Tripathi, Ratan Chopra, Heikham Russiachand Singh, Vikas Belamkar, Pardeep Kumar Bhardwaj, Jeff J. Doyle, Ashley N. Egan