Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

New Data, Old Story: Molecular Data Illuminate the Tribal Relationships among Rove Beetles of the Subfamily Staphylininae (Coleoptera: Staphylinidae)

“…The site-heterogeneous model CAT-GTR was implemented in phylobayes mpi 1.7 [30,31] run on the University of Bristol BlueCrystal Phase3 Cluster. Two independent Markov chain Monte Carlo (MCMC) chains were run until convergence.…”

“…With this feature, CAT-GTR has been shown to fit many molecular datasets better than conventional site-homogeneous models [41]. Because it alleviates common artefacts such as long branch attraction [30,31], site-heterogeneous models have been used to resolve long-standing phylogenetic controversies such as the relationships between prokaryotes, archaea, and eukaryotes [32], or the basal branching order within Metazoa [33,34].…”

Peer Review #2 of "Comparative genomic analysis of the principal Cryptosporidium species that infect humans (v0.1)"

“…Advances in DNA sequencing technologies and bioinformatics have promoted the routine use of complete genome sequences, revolutionizing the study of both model and non-model organisms, particularly in microbiology (Young & Gillung, 2020). Phylogenomic is one of the numerous disciplines that have taken advantage of the progress in NGS technologies, using the massive datasets to infer both phylogenetic relationships between taxa, improving the understanding of molecular evolution, and putative functions for DNA or protein sequences (Young & Gillung, 2020). A phylogenomic analysis is being applied now to validate previous findings with classic singlemarker molecular methods and to resolve with unprecedented resolution, the phylogenetic relationships between species and isolates of the human infecting Cryptosporidium parasites (Glaberman et al, 2001;Abe & Makino, 2010;Abal-Fabeiro et al, 2013;Wagnerová et al, 2015;Pérez-Cordón et al, 2016).…”

<p class="ZootaxaTitle">Hurdles in fungal taxonomy: Effectiveness of recent methods in discriminating taxa

“…Phylogenetics is a dynamic discipline that reconstructs and analyses the evolutionary relationships of species or taxa (Wiley & Lieberman 2011;Young & gillung 2020). Initially, most phylogenetic papers were based on nuclear ribosomal RNA genes (rDNA) (Bruns et al 1991;Hibbett 1992;Hwang & Kim 1999;Schoch et al 2009Schoch et al , 2012 as these multicopy genes are highly conserved within a species and can vary among species (Bruns et al 1991;Hibbett 1992;xu 2006).…”