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153 Publications visible to you, out of a total of 153
Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

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Abstract Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic‐placement methods …ogenetic‐placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA‐ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA‐ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA‐ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.

Authors: Isabelle Ewers, Lubomír Rajter, Lucas Czech, Frédéric Mahé, Alexandros Stamatakis, Micah Dunthorn

Date Published: 1st Sep 2023

Publication Type: Journal

Simulations of sequence evolution: how (un)realistic they are and why

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Abstract Motivation Simulating Multiple Sequence Alignments (MSAs) using probabilistic models of sequence evolution plays an important role in the evaluation of phylogenetic inference tools, and is …luation of phylogenetic inference tools, and is crucial to the development of novel learning-based approaches for phylogenetic reconstruction, for instance, neural networks. These models and the resulting simulated data need to be as realistic as possible to be indicative of the performance of the developed tools on empirical data and to ensure that neural networks trained on simulations perform well on empirical data. Over the years, numerous models of evolution have been published with the goal to represent as faithfully as possible the sequence evolution process and thus simulate empirical-like data. In this study, we simulated DNA and protein MSAs under increasingly complex models of evolution with and without insertion/deletion (indel) events using a state-of-the-art sequence simulator. We assessed their realism by quantifying how accurately supervised learning methods are able to predict whether a given MSA is simulated or empirical. Results Our results show that we can distinguish between empirical and simulated MSAs with high accuracy using two distinct and independently developed classification approaches across all tested models of sequence evolution. Our findings suggest that the current state-of-the-art models fail to accurately replicate several aspects of empirical MSAs, including site-wise rates as well as amino acid and nucleotide composition. Data and Code Availability All simulated and empirical MSAs, as well as all analysis results, are available at https://cme.h-its.org/exelixis/material/simulation_study.tar.gz . All scripts required to reproduce our results are available at https://github.com/tschuelia/SimulationStudy and https://github.com/JohannaTrost/seqsharp . Contact julia.haag@h-its.org

Authors: Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau

Date Published: 12th Jul 2023

Publication Type: Journal

Quantitative Analysis and Characterization of Natural Language Evolution Datasets

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Methods for phylogenetic inference have been developed mainly for the reconstruction of evolutionary relationships of species based on biological sequence data. However, these methods are also made use … of in linguistics for inferring phylogenies concerning the evolution of natural languages. In the scope of this thesis, we examine the corresponding linguistic input data. We conduct a case study on an exemplary morphosyntactic data set, examining various methods to analyze the signal it contains and to eliminate geographical information the data may include. Further, we perform analyses on numerous linguistic data sets collected from various sources and assembled in a database. We compare these data sets to morphological data from biology, considering differences in the behavior of phylogenetic inferences with RAxML-NG. Additionally, we investigate how it impacts the tree inferences, whether we represent a data set by a binary or by a multi-valued MSA. We study how to model subjectivity related with synonym selection in cognate data. We present probabilistic MSAs as a possible solution and show on an example data set that this might be an appropriate approach

Authors: Luise Häuser, Julia Haag, Alexandros Stamatakis

Date Published: 17th Jun 2023

Publication Type: Master's Thesis

Parallel Inference of Phylogenetic Stands with Gentrius

Abstract

Not specified

Authors: Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis

Date Published: 1st May 2023

Publication Type: Proceedings

The power and limitations of species tree-aware phylogenetics

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Abstract Species tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including the duplication, transfer and loss of genes. …fer and loss of genes. Over the past ten years these methods have emerged as a powerful tool for inferring and rooting gene and species trees, inferring ancestral gene repertoires, and studying the processes of gene and genome evolution. However, these methods are complex and can be more difficult to use than traditional phylogenetic approaches. Method development is rapid, and it can be difficult to decide between approaches and interpret results. Here, we review ALE and GeneRax, two popular packages for reconciling gene and species trees, explaining how they work, how results can be interpreted, and providing a tutorial for practical analysis. It was recently suggested that reconciliation-based estimates of duplication and transfer frequencies are unreliable. We evaluate this criticism and find that, provided parameters are estimated from the data rather than being fixed based on prior assumptions, reconciliation-based inferences are in good agreement with the literature, recovering variation in gene duplication and transfer frequencies across lineages consistent with the known biology of studied clades. For example, published datasets support the view that transfers greatly outnumber duplications in most prokaryotic lineages. We conclude by discussing some limitations of current models and prospects for future progress. Significance statement Evolutionary trees provide a framework for understanding the history of life and organising biodiversity. In this review, we discuss some recent progress on statistical methods that allow us to combine information from many different genes within the framework of an overarching phylogenetic species tree. We review the advantages and uses of these methods and discuss case studies where they have been used to resolve deep branches within the tree of life. We conclude with the limitations of current methods and suggest how they might be overcome in the future.

Authors: Tom A. Williams, Adrian A. Davin, Benoit Morel, Lénárd L. Szánthó, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szöllősi

Date Published: 17th Mar 2023

Publication Type: Journal

Is there a Correlation between the Use of Swearwords and Code Quality in Open Source Code?

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One of the most fundamental unanswered questions that has been bothering mankind during the Anthropocene is whether the use of swearwords in open source code is positively or negatively correlated with … source code quality. To investigate this profound matter we crawled and analysed over 3800 C open source code containing English swearwords and over 7600 C open source code not containing swearwords from GitHub. Subsequently, we quantified the adherence of these two distinct sets of source code to coding standards, which we deploy as a proxy for source code quality via the SoftWipe tool developed in our group. We find that open source code containing swearwords exhibit significantly better code quality than those not containing swearwords under several statistical tests. We hypothesise that the use of swearwords constitutes an indicator of a profound emotional involvement of the programmer with the code and its inherent complexities, thus yielding better code based on a thorough, critical, and dialectic code analysis process.

Authors: Jan Strehmel, Ben Bettisworth, Dimitri Höhler, Alexandros Stamatakis

Date Published: 1st Feb 2023

Publication Type: Bachelor's Thesis

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

Abstract

Not specified

Authors: Dilek Koptekin, Eren Yüncü, Ricardo Rodríguez-Varela, N. Ezgi Altınışık, Nikolaos Psonis, Natalia Kashuba, Sevgi Yorulmaz, Robert George, Duygu Deniz Kazancı, Damla Kaptan, Kanat Gürün, Kıvılcım Başak Vural, Hasan Can Gemici, Despoina Vassou, Evangelia Daskalaki, Cansu Karamurat, Vendela K. Lagerholm, Ömür Dilek Erdal, Emrah Kırdök, Aurelio Marangoni, Andreas Schachner, Handan Üstündağ, Ramaz Shengelia, Liana Bitadze, Mikheil Elashvili, Eleni Stravopodi, Mihriban Özbaşaran, Güneş Duru, Argyro Nafplioti, C. Brian Rose, Tuğba Gencer, Gareth Darbyshire, Alexander Gavashelishvili, Konstantine Pitskhelauri, Özlem Çevik, Osman Vuruşkan, Nina Kyparissi-Apostolika, Ali Metin Büyükkarakaya, Umay Oğuzhanoğlu, Sevinç Günel, Eugenia Tabakaki, Akper Aliev, Anar Ibrahimov, Vaqif Shadlinski, Adamantios Sampson, Gülşah Merve Kılınç, Çiğdem Atakuman, Alexandros Stamatakis, Nikos Poulakakis, Yılmaz Selim Erdal, Pavlos Pavlidis, Jan Storå, Füsun Özer, Anders Götherström, Mehmet Somel

Date Published: 2023

Publication Type: Journal

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