Lucas Czech
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View article: ybyra: Y-chromosome haplogroup calling using a tree-based scoring method
ybyra: Y-chromosome haplogroup calling using a tree-based scoring method Open
Summary We present ybyra , a Snakemake workflow for automated Y-chromosome haplogroup assignment using a tree-based scoring method with robust and transparent heuristics. The pipeline supports both human reference genome builds 37 and 38, …
View article: Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana
Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana Open
Climate change is threatening species with extinction, and rapid evolutionary adaptation may be their only option for population rescue over short ecological timescales. However, direct observations of rapid genetic adaptation and populati…
View article: Population and adaptation history of 739<i>Thlaspi arvense</i>natural accessions
Population and adaptation history of 739<i>Thlaspi arvense</i>natural accessions Open
Pennycress ( Thlaspi arvense ) is a promising intermediate oilseed crop, producing oil suitable for conversion to biofuels—including aviation fuels. While domestication efforts are ongoing, a deeper understanding of the genetic architectur…
View article: grenedalf: population genetic statistics for the next generation of pool sequencing
grenedalf: population genetic statistics for the next generation of pool sequencing Open
Summary Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversit…
View article: Interpreting phylogenetic placements for taxonomic assignment of environmental <scp>DNA</scp>
Interpreting phylogenetic placements for taxonomic assignment of environmental <span>DNA</span> Open
Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic‐placement methods represent two alternative approaches to taxono…
View article: grenedalf: population genetic statistics for the next generation of pool sequencing
grenedalf: population genetic statistics for the next generation of pool sequencing Open
Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity in wil…
View article: Power and limitations of the mutations-area relationship to assess within-species genetic diversity targets for post-2020 Sustainable Development Goals
Power and limitations of the mutations-area relationship to assess within-species genetic diversity targets for post-2020 Sustainable Development Goals Open
To evaluate the United Nation’s preliminary post-2020 sustainable goals on protecting high levels of genetic diversity per species, Exposito-Alonso et al. (2022) proposed a new framework to predict a species’ loss of genetic diversity give…
View article: Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs
Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs Open
Taxonomic assignment of OTUs is an important bioinformatics step in analyzing environmental sequencing data. Pairwise-alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their res…
View article: Wide-ranging consequences of priority effects governed by an overarching factor
Wide-ranging consequences of priority effects governed by an overarching factor Open
Priority effects, where arrival order and initial relative abundance modulate local species interactions, can exert taxonomic, functional, and evolutionary influences on ecological communities by driving them to alternative states. It rema…
View article: Author response: Wide-ranging consequences of priority effects governed by an overarching factor
Author response: Wide-ranging consequences of priority effects governed by an overarching factor Open
Article Figures and data Abstract Editor's evaluation Introduction Results and discussion Materials and methods Appendix 1 Appendix 2 Data availability References Decision letter Author response Article and author information Metrics Abstr…
View article: grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads
grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads Open
Summary We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls. Our pipeline offers a range of popular sof…
View article: Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade Open
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) metho…
View article: pH as an eco-evolutionary driver of priority effects
pH as an eco-evolutionary driver of priority effects Open
Priority effects, where arrival order and initial relative abundance modulate local species interactions, can exert taxonomic, functional, and evolutionary influences on ecological communities by driving them to alternative states. It rema…
View article: Metagenomic Analysis using Phylogenetic Placement -- A Review of the\n First Decade
Metagenomic Analysis using Phylogenetic Placement -- A Review of the\n First Decade Open
Phylogenetic placement refers to a family of tools and methods to analyze,\nvisualize, and interpret the tsunami of metagenomic sequencing data generated\nby high-throughput sequencing. Compared to alternative (e. g.,\nsimilarity-based) me…
View article: Monitoring rapid evolution of plant populations at scale with Pool-Sequencing
Monitoring rapid evolution of plant populations at scale with Pool-Sequencing Open
The change in allele frequencies within a population over time represents a fundamental process of evolution. By monitoring allele frequencies, we can analyze the effects of natural selection and genetic drift on populations. To efficientl…
View article: Genetic diversity loss in the Anthropocene
Genetic diversity loss in the Anthropocene Open
More species than ever before are at risk of extinction due to anthropogenic habitat loss and climate change. But even species that are not threatened have seen reductions in their populations and geographic ranges, likely impacting their …
View article: Swarm v3: towards tera-scale amplicon clustering
Swarm v3: towards tera-scale amplicon clustering Open
Motivation Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3…
View article: grenepipe: A flexible, scalable, and reproducible pipeline to automate variant and frequency calling from sequence reads
grenepipe: A flexible, scalable, and reproducible pipeline to automate variant and frequency calling from sequence reads Open
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to s…
View article: Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult
Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult Open
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by examp…
View article: The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils
The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils Open
Dinophytes are widely distributed in marine‐ and fresh‐waters, but have yet to be conclusively documented in terrestrial environments. Here, we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neo…
View article: <scp>SCRAPP</scp> : A tool to assess the diversity of microbial samples from phylogenetic placements
<span>SCRAPP</span> : A tool to assess the diversity of microbial samples from phylogenetic placements Open
Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogeneti…
View article: The windblown: possible explanations for dinophyte DNA in forest soils
The windblown: possible explanations for dinophyte DNA in forest soils Open
Dinophytes are widely distributed in marine- and fresh-waters, but have yet to be conclusively documented in terrestrial environments. Here we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neot…
View article: Phylogenetic analysis of SARS-CoV-2 data is difficult
Phylogenetic analysis of SARS-CoV-2 data is difficult Open
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org . Here, we review the difficulties of inferring reliable phylogenies by exam…
View article: SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements
SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements Open
Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogeneti…
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data Open
View article: Novel Methods for Analyzing and Visualizing Phylogenetic Placements
Novel Methods for Analyzing and Visualizing Phylogenetic Placements Open
Die DNS (englisch: DNA) bildet die vererbbare Grundlage allen bekannten Lebens auf dem Planeten. Entsprechend wichtig ist ihre "Entschlüsselung" für die Biologie im Allgemeinen, und für die Erforschung der evolutionären Zusammenhänge versc…
View article: Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence
Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence Open
Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set o…
View article: Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples Open
Background: The exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutiona…
View article: Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity Open
High-throughput environmental DNA metabarcoding has revolutionized the analysis of microbial diversity, but this approach is generally restricted to amplicon sizes below 500 base pairs. These short regions contain limited phylogenetic sign…
View article: Methods for automatic reference trees and multilevel phylogenetic placement
Methods for automatic reference trees and multilevel phylogenetic placement Open
Motivation In most metagenomic sequencing studies, the initial analysis step consists in assessing the evolutionary provenance of the sequences. Phylogenetic (or Evolutionary) Placement methods can be employed to determine the evolutionary…