L. Czech

Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs

This study compares taxonomic assignments of ciliate OTUs using pairwise alignment and phylogenetic placement methods, showing differences when OTUs have low similarity to reference databases.

Structural and functional analysis of YopR and identification of an additional key component of the SPβ phage lysis-lysogeny management system

The paper identifies YopR and YosL as key components of the SPβ phage lysis-lysogeny system, showing YopR's DNA-binding role and YosL's necessity for lytic cycle induction.

pH as an eco-evolutionary driver of priority effects

This study identifies pH as a key factor driving priority effects in nectar microbial communities, influencing species interactions, evolution, and plant reproduction.

Monitoring rapid evolution of plant populations at scale with Pool-Sequencing

This paper validates pool-sequencing for tracking rapid plant population evolution and introduces tools to accelerate population genetic analysis.

Genetic diversity loss in the Anthropocene

The paper introduces a mathematical framework to estimate genetic diversity loss due to habitat reduction and shows that over 10% of genetic diversity may already be lost globally.

The windblown: possible explanations for dinophyte DNA in forest soils

The paper analyzes environmental DNA metabarcoding data to show dinophyte DNA in forest soils likely comes from windblown aquatic species, not active terrestrial residents.

Phylogenetic analysis of SARS-CoV-2 data is difficult

The paper reviews challenges in inferring reliable SARS-CoV-2 phylogenies due to high sequence similarity and low mutation rates, highlighting difficulties in rooting and classification.

Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

This study uses long-read sequencing to analyze eukaryotic rDNA operons, improving phylogenetic resolution and taxonomic classification of environmental DNA.

Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence

The paper introduces quartet-based measures to quantify phylogenetic incongruence, showing they are more accurate and robust than bipartition-based methods, especially with partial trees and missing data.

A Critical Review on the Use of Support Valuesin Tree Viewers and Bioinformatics Toolkits

This paper reviews issues with branch support values in phylogenetic tree viewers and toolkits, finding that 14/20 tools lack user control over node label semantics, leading to potential errors in tree re-rooting.

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites

The paper investigates protist diversity in Neotropical rainforest soils, finding them hyperdiverse and dominated by parasitic Apicomplexa, which may influence animal diversity.