58 results match your criteria: "Institute for Theoretical Informatics[Affiliation]"

Estimating the statistical robustness of the inferred tree(s) constitutes an integral part of most phylogenetic analyses. Commonly, one computes and assigns a branch support value to each inner branch of the inferred phylogeny. The still most widely used method for calculating branch support on trees inferred under maximum likelihood (ML) is the Standard, nonparametric Felsenstein bootstrap support (SBS).

View Article and Find Full Text PDF

Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes.

Forensic Sci Int Genet

July 2024

Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece.

Article Synopsis
  • The Battle of Crete during WWII saw German forces suffer substantial civilian resistance, leading to mass executions as retribution, including the execution of 18 males in the village of Adele.
  • This study is the first of its kind in Greece, identifying the victims' skulls through a request from the local community and utilizing advanced techniques like ancient DNA analysis and genome skimming.
  • The findings highlight the methodology as a promising forensic tool for identifying war victims from degraded DNA, offering potential for similar applications in Greece and other conflict zones.
View Article and Find Full Text PDF

Complexity of avian evolution revealed by family-level genomes.

Nature

May 2024

Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.

Article Synopsis
  • Relationships among avian lineages remain unresolved due to factors like species diversity, phylogenetic methods, and selection of genomic regions.
  • An analysis of 363 bird species' genomes reveals a well-supported evolutionary tree but highlights significant discrepancies among certain groups.
  • Findings suggest that after the Cretaceous-Palaeogene extinction, birds experienced increased population size and diversification, which offers a new foundational understanding for future research in avian evolution.
View Article and Find Full Text PDF
Article Synopsis
  • Genomes provide valuable insights into evolution, and current research aims to improve phylogenetic methods that accurately model both gene trees and the shared species tree, addressing uncertainties in these processes.
  • AleRax is a new software designed to infer reconciled gene trees alongside a species tree using a robust probabilistic model that handles gene duplication, transfer, and loss, while efficiently managing uncertainty in the data.
  • The software outperforms other gene tree inference tools in speed and accuracy, successfully processing multiple gene families to help researchers test different phylogenetic hypotheses and analyze large datasets.
View Article and Find Full Text PDF
Article Synopsis
  • This study focuses on simulating multiple sequence alignments using probabilistic models to improve phylogenetic reconstruction tools, like neural networks.
  • The researchers created DNA and protein MSAs through complex evolutionary models and evaluated their realism against empirical data.
  • Results indicated that while they could distinguish between real and simulated alignments effectively, existing simulation models do not fully capture key characteristics of actual biological sequences.
View Article and Find Full Text PDF
Article Synopsis
  • * Research shows that by adjusting specific numerical thresholds in tools like RAxML-NG and IQ-TREE, tree inference times can be significantly improved without compromising the accuracy of the resulting trees.
  • * The study provides access to datasets and scripts used in the research, allowing others to replicate or build upon their findings via the provided links.
View Article and Find Full Text PDF
Article Synopsis
  • - ALE and GeneRax are tools designed for analyzing how gene trees relate to species trees, using statistical models to understand events like gene duplication, transfer, and loss, while also helping to determine the origins of gene families and root species trees.
  • - Despite recent criticisms regarding their reliability in estimating gene duplication and transfer events, a study found that ALE and GeneRax perform well on both simulated data and real-world empirical data.
  • - Specifically, ALE demonstrates a consistent ability to capture variations in gene event frequencies according to known biological contexts, successfully rooting species trees in plants and opisthokonts, while providing comparable insights for Bacteria.
View Article and Find Full Text PDF
Article Synopsis
  • The study explores two methods for assigning taxonomic classifications to operational taxonomic units (OTUs) from environmental sequencing data: VSEARCH (pairwise alignment) and EPA-ng (phylogenetic placement), highlighting differences in their results.
  • It finds that discrepancies between the two methods mainly occur when OTUs have low similarity to reference databases, suggesting potential challenges in accurate taxonomic classification at the subtaxon level.
  • The research emphasizes using GAPPA alongside EPA-ng for better evaluation of taxonomic assignments, particularly in cases with multiple placement options, and integrates evolutionary and ecological insights of the studied colpodean OTUs.
View Article and Find Full Text PDF
Article Synopsis
  • Researchers used methods from molecular evolution to calculate exact win probabilities for knockout tournaments instead of using slower simulations.
  • Their new open-source code is significantly faster, offering improvements two orders of magnitude faster than simulating and over two times faster than traditional methods.
  • They can now quickly assess prediction uncertainty by running extensive analyses, even for larger tournaments, on standard laptops in just minutes.
View Article and Find Full Text PDF
Article Synopsis
  • The DEC model of biogeography is computationally intensive, requiring significant processing time for large datasets, limiting analyses based on the number of regions.
  • The newly developed tool, Lagrange-NG, offers up to 49 times faster performance with multithreading and 26 times faster with a single thread, enabling efficient analysis of up to 12 regions in about 18 minutes.
  • Lagrange-NG not only improves computational speed by using Krylov subspaces for matrix exponential calculations, but also adheres to higher coding quality standards, making it a reliable and accessible tool for researchers under GPL2.
View Article and Find Full Text PDF
Article Synopsis
  • Missing data and incomplete lineage sorting (ILS) make it hard to accurately infer species trees, leading to the development of methods like ASTRAL and ASTRID to handle ILS but struggle with high missing data.
  • Asteroid is a new algorithm for inferring unrooted species trees from unrooted gene trees that outperforms ASTRAL and ASTRID in cases with over 80% missing data and operates much faster with large datasets.
  • Asteroid is available for free online at GitHub, along with supplementary information accessible through Bioinformatics.
View Article and Find Full Text PDF

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.

Curr Biol

January 2023

Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey; Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. Electronic address:

Article Synopsis
  • - The study maps human genetic diversity across regions like Anatolia, Iran, and the Aegean, highlighting changes from the early Neolithic period to more complex societal structures using a combination of ancient and modern genomes.
  • - Findings reveal that genetic diversity increased over time, with early Holocene populations in Southwest Asia and the East Mediterranean becoming more similar, followed by a divergence starting in the Bronze Age due to external gene flow, described as "the expanding mobility model."
  • - The research also uncovers a trend of increasing male bias in admixture events throughout the Holocene, which is measured using specific genetic distance methods that are more effective than traditional F statistics.
View Article and Find Full Text PDF
Article Synopsis
  • Phylogenetic analysis using the Maximum-Likelihood model is complex and requires significant time and resources, as it involves inferring multiple independent trees from datasets.
  • Depending on the dataset, results can show consistent tree structures or vastly different topologies that are statistically similar, but current methods can't predict which will happen.
  • The new tool Pythia, a Random Forest Regressor, helps quantify the difficulty of analyzing datasets in terms of expected signal and uncertainty, allowing researchers to choose suitable analysis setups and algorithms based on the dataset's complexity.
View Article and Find Full Text PDF
Article Synopsis
  • Phylogenetic placement involves using unique tools and methods to analyze metagenomic sequencing data, providing a more accurate context for metabarcoding sequences by considering evolutionary history.
  • This approach enhances metagenomic surveys by allowing researchers to work with sequences even if they don't match existing databases closely, and it supports various analyses like species community dynamics and environmental correlations.
  • The review highlights the progress made in the last decade, aiming to encourage the use of phylogenetic placement, detail the workflow from raw data to publishable results, and provide insight into common tools, challenges, and effective data interpretation strategies.
View Article and Find Full Text PDF
Article Synopsis
  • Phylogenetic networks are used to model complex evolutionary scenarios, but existing methods struggle with high computational demands and small datasets, especially when considering incomplete lineage sorting (ILS).
  • The team introduces NetRAX, a maximum likelihood tool that simplifies network inference by avoiding ILS complications, utilizing efficient tree likelihood computations, and outputting results in Extended Newick format.
  • NetRAX performs well on simulated data, providing accurate network inference quickly, and is available for use under an open-source license on GitHub.
View Article and Find Full Text PDF
Article Synopsis
  • - CellPhy is a new framework that helps scientists deduce the evolutionary relationships of cells by analyzing genetic mutations (single-nucleotide variants) in single cells while addressing common errors in this data.
  • - This tool uses a specific model to manage different genetic states and errors that can arise during genetic analysis, integrating seamlessly with a well-known program called RAxML-NG, which is ideal for handling large volumes of data.
  • - Simulations show that CellPhy is not only faster but also more accurate than current leading methods when working with single-cell genomic data, making it a valuable resource for researchers.
View Article and Find Full Text PDF
Article Synopsis
  • Species tree inference from gene family trees is gaining popularity as it addresses differences between species trees and gene family trees, particularly using methods that handle multiple-copy gene families.
  • The authors present SpeciesRax, a new maximum likelihood method that accurately infers rooted species trees while accounting for gene duplications, losses, and transfers.
  • SpeciesRax demonstrates both high accuracy and speed, processing data from 188 vertebrate species in just one hour using 40 cores, and is available for public use on GitHub and BioConda.
View Article and Find Full Text PDF
Article Synopsis
  • Scientists often struggle to set accurate parameters for simulating evolutionary trees in their research, which makes it challenging to assess new phylogenetic models.
  • To address this, a new database named 'RAxML Grove' has been introduced, featuring over 60,000 inferred trees along with model parameter estimates from anonymized datasets analyzed using RAxML.
  • RAxML Grove is freely accessible online, and its applications can help researchers design realistic simulations and analyze tree shape distributions effectively.
View Article and Find Full Text PDF

SPART: A versatile and standardized data exchange format for species partition information.

Mol Ecol Resour

January 2022

Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.

Article Synopsis
  • A variety of data types and computer tools exist for species delimitation (SD), but these methods are not commonly used by alpha-taxonomists due to challenges like lack of compatibility among different SD programs.
  • Researchers often face time-consuming processes when comparing species partitions from different SD approaches due to their varying results and the absence of a standard format.
  • The proposed standardized format, SPART, aims to improve compatibility among SD tools by reporting partitions and individual assignments, with options for including support values and original analysis details, while providing two user-friendly versions: matricial SPART and SPART.XML.
View Article and Find Full Text PDF
Article Synopsis
  • Scientific software is crucial for gaining new insights in research, but its coding standards are often not evaluated.
  • Poor coding practices can result in incorrect scientific outcomes, highlighting the importance of assessment.
  • To address this, SoftWipe is an open-source tool that ranks 48 computational tools based on coding standards adherence, aiding in software review and selection.
View Article and Find Full Text PDF

The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics.

Mol Phylogenet Evol

June 2021

Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece.

Article Synopsis
  • * Mitochondrial DNA studies have categorized these species into two main subgroups: "P. tauricus" and "P. erhardii," highlighting the genetic relationships among them.
  • * By using advanced genetic sequencing methods, researchers confirmed the existence of all recently recognized species and identified at least two additional species within the groups, suggesting a need for re-evaluating the taxonomy of Podarcis in this region.
View Article and Find Full Text PDF
Article Synopsis
  • Many daily publications focus on analyzing SARS-CoV-2 data, including phylogenetic studies available on nextstrain.org.
  • The authors discuss challenges in creating reliable phylogenies due to a high number of virus sequences but a low number of mutations, making it tough to draw clear evolutionary connections.
  • They conclude that while phylogenetic methods can offer some insights into COVID-19's evolution and spread, researchers should interpret results with caution, especially when using standard analysis tools.
View Article and Find Full Text PDF

Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage.

View Article and Find Full Text PDF
Article Synopsis
  • Microbial ecology research is advancing due to cheaper DNA sequencing and better data analysis methods, particularly through phylogenetic placement, which identifies unknown sequences based on a reference tree.
  • A new tool called scrapp has been developed to analyze microbial diversity more effectively, utilizing a molecular species delimitation algorithm and a novel clustering approach to manage large data sets.
  • Evaluation of scrapp with both simulated and real-world data shows it performs as well or better than existing methods in classifying samples based on diversity features, making it a valuable resource for researchers.
View Article and Find Full Text PDF
Article Synopsis
  • Inferring phylogenetic trees for individual gene families is challenging due to short alignments and ineffective substitution models, so methods that incorporate species tree information are necessary.
  • GeneRax is introduced as the first maximum likelihood software that considers both sequence-level and gene-level events, such as duplications and transfers, for phylogenetic inference.
  • In simulations, GeneRax accurately infers trees in 90% of cases and is the fastest method for empirical data, effectively performing large-scale analyses, as demonstrated by its ability to process 1,099 Cyanobacteria families in just 8 minutes.
View Article and Find Full Text PDF