Tag: BEAST

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015). Article  Google Scholar  Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019). ADS  CAS  PubMed  Article  Google…

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

Substitution model selection in BEAST 1 I have constructed phylogenomic tree using the protein-coding genes of plant mitogenome using maximum likelihood method. Now I want to compare it using Bayesian method using BEAST. The alignment file is amino acids instead of DNA. What is the best recommendation of substitution model…

Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, et al. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol. 2020;6:2. doi.org/10.1093/ve/veaa048. Article  Google Scholar  Chen J, Han Z, Wu H, Xu W, Yu D, Zhang Y. A large-scale outbreak…

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed  Google Scholar  Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed  Google Scholar  Rosenqvist G, Berglund A. Sexual signals and mating…

Mah, C. L. & Blake, D. B. Global diversity and phylogeny of the asteroidea (Echinodermata). PLoS ONE 7, e35644. doi.org/10.1371/journal.pone.0035644 (2012). ADS  CAS  Article  PubMed  PubMed Central  Google Scholar  WoRMS. Asteroidea. Accessed at: www.marinespecies.org/aphia.php?p=taxdetails&id=123080. on 2021-08-02. Blake, D. B. Adaptive zones of the class Asteroidea (Echinodermata). Bull. Mar. Sci. 46,…

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

If you’ve tried OpenAPI spec generators, you know how it goes. They get you about 60-80% there, but you end up having to modify the code by hand. For one of the specs (GitHub REST API spec), a popular code generator I tried produced more than 300 compile-time errors. With…

Dataset construction, cluster identification and definition of DCCs Whole genome sequencing of two collections of isolates from Manchester, UK, and the Netherlands was carried out as previously described2. Briefly, DNA was extracted from colony sweeps of subcultured samples before to paired-end sequencing using the Illumina HiSeq platform. These samples were…

This repo gathers all the input files and scripts related to our study entitled “Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020” (Bollen et al. submitted): R scripts to prepare, analyse, and visualise the phylogeographic analyses performed in this study, Geographic Information…

1. Dudas, G. et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544, 309–315 (2017). ADS  CAS  Article  Google Scholar  2. Kafetzopoulou, L. E. et al. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 363, 74–77 (2019). ADS  CAS  Article …

Identification and analysis of the early transmission dynamics, importations and local circulation of SARS-CoV-2 in Ecuador inferred from genomic data. Bernardo Gutierrez1,2, Sully Márquez3, Belén Prado-Vivar3, Mónica Becerra-Wong3, Juan José Guadalupe4, Darlan da Silva Candido1, Juan Carlos Fernandez-Cadena5, Gabriel Morey-Leon6, Rubén Armas-Gonzalez7, Derly Madeleiny Andrade-Molina5, Alfredo Bruno8,9, Domenica de Mora8,…

If science fiction has taught us anything over the years, it’s that there stands an inherent danger whenever humankind decides to play God. And yet the temptation to seek progress, to satiate curiosity, and gain knowledge is often too strong to ignore. Sometimes, these desires can lead to some truly fascinating innovations….

Gromacs 4.5.4 manual OntheStabilityofNegativelyChargedPlatelets inCalcium g_energy(1) [debian man page] Gromacs User Manual Version 4.6The defence of Königsberg had cost the lives of 42,000 German soldiers and 25,000 civilians. He yanked the seaman out and shouted at him to report straight to…

Job DescriptionThe University of Maryland, Baltimore (UMB), Institute of Human Virology (IHV) is currently recruiting for a Senior Bioinformatics Analyst. The Senior Bioinformatics Analyst provides complex support to Principal Investigator in the Division of Epidemiology and Prevention. The range of duties include, but are not restricted to, designing statistical analysis,…

“Simplifing” a very fragmented genome for visualisation? 1 Hi there, I have a very fragmented reference genome that i want to visualize (with jbrowse or similar) this is the paper for the genome: link here the genome can be found: link2 here are the quast statistics: ######## QUAST Results ########…

The genesis of the Loch Ness Monster has been discovered in a “plausible theory” of what the mythological beast is. The enigma of the Loch Ness Monster has perplexed scholars and visitors for decades, and a team of international scientists has discovered no trace of the aquatic reptile assumed to…