IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.This work was supported by the Austrian Science Fund (Grant No. I-2805-B29) to A.v.H. and by the Australian National University Futures Scheme grant to R.L

De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus

The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus

An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex

Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the “Mediterranean” (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the “African silver-leafing” (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the “ASL” does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies

Phylogenomics

In der Evolutionsbiologie wurde in den letzten Jahren durch Aufkommen der Phylogenomik ein neues Kapitel aufgeschlagen. Mit Hilfe genomweiter Analysen wird es zunehmend möglich, schwierige Fragestellungen zur Evolutionsgeschichten zu untersuchen, doch diese neuen Perspektiven sind gleichzeitig verbunden mit erhöhter Komplexität und anderen Schwierigkeiten bei der Stammbaumberechnung. Der Fokus dieser Dissertation ist es, Einblicke in Fragen aus der Theorie der Baumrekonstruktion sowie zu Algorithmen und Anwendungen der Phylogenomik zu geben. Ein Hauptaugenmerk liegt hierbei auf der Untersuchung phylogenetischer Terrassen, dies Speziesbäume mit gleichen Maximum Likelihood oder Maximum Parsimonie Werten. Ein Problem bei der Suche nach optimalen Bäumen ist die Größe der Terrasse. Die Größe der Terrassen hängt dabei entscheidend von dem untersuchten multiple Sequenz Alignment ab. Im Rahmen dieser Arbeit wird zunächst erklärt wie man Terrassen während der Baumsuche detektiert. Dazu studieren wir durch Partitionen induzierte Bäume und in welcher Weise topologische Umformungen am Speziesbaum Änderungen an den Partitionsbäumen bedingen. Sollte eine Änderung der Verzweigungsstruktur eines Speziesbaum keine Änderung an den mit ihm assoziierten induzierten Partitionsbäumen hervorrufen, gehören sowohl der gegenwärtige als auch der geänderte neue Speziesbaum zur selben Terrasse. Es werden drei Propositionen bewiesen, die Kriterien definieren nach welchen verschiedene Umformungsoperationen, namentlich NNI (Nearest Neighbour Interchange), SPR (Subtree Pruning and Regrafting) und TBR (Tree Bisection and Reconnection), sich die induzierten Partitionsbäume verändern. Weiters wird das Konzept von Terrassen erweitert, in dem partielle Terrassen definiert werden und ihr Auftreten für echte Alignments unter NNI Umformungsoperationen untersucht wird. Im zweiten Teil wird die Datenstruktur, PTA, (phylogenetic terrace aware data structure) vorgestellt, die eine effiziente Analyse verknüpfter multipler Alignments unter Berücksichtigung phylogenetischer Terrassen ermöglicht. Mit Hilfe von PTA und den Kriterien zur Erfassung (partieller) Terrassen ist es möglich, überflüssige Neuberechnungen der Maximum Likelihood oder Maximum Parsimonie Werte zu vermeiden und so die für die Baumsuche benötigte Rechenzeit zu verringern. Durch die Identifizierung partieller Terrassen wird im Vergleich zur Standardimplementierung eine bis zu 5-fache Beschleunigung von IQ-TREE festgestellt und nach der Implementierung der Terrassenidentifikation ist IQ-TREE in der Lage bis zu 6 Mal schneller Maximum-Likelihood-Bäume zu finden als RAxML. Die Datenstruktur PTA eignet sich für den Einsatz mit allen Partitionsmodellen und für alle üblichen topologischen Umformungen wie NNI, SPR und TBR. Im Schlussteil dieser Arbeit werden Methoden für den Einsatz in Naturschutzbiologie und -ökologie eingeführt und diskutiert, wobei Phylogenomik herangezogen wird, um die evolutionäre Diversität verschiedener Spezies zu quantifizieren. Wir diskutieren die Aufgabe der Auswahl überlebensfähiger Taxa, ein Optimierungsproblem unter Einbeziehung von Räuber-Beute-Interaktionen. Zuerst wird dabei der Rahmen der Aufgabenstellung erweitert, um auch die Splitdiversität (SD) zu erfassen, ein Biodiversitätsmaß welches auf der evolutionären Distanz zwischen verschiedenen Spezies in Splitnetzwerken basiert. Danach erweitern wir die Definition von Lebensfähigkeit um die Nahrungszusammensetzung des Räubers miteinzubeziehen und so die Modellierung realistischer zu gestalten. Mit Hilfe der SD und unter Berücksichtigung eines realistischen Modells werden Spezies für Naturschutzmaßnahmen priorisiert. Obwohl derartige Optimierungsaufgaben in den Bereich NP-schwerer Probleme fallen, zeige ich, dass sie mit Hilfe von ILP (Integer Linear Programming) in überschaubarer Zeit gelöst werden können. In dieser Arbeit werden ILP-Ansätze für alle darin diskutierten Problemstellungen beschrieben sowie eine Implementierung im Software Paket PDA bereitgestellt.In the recent years phylogenomics opened a new chapter in evolutionary biology. The analysis of the genome-scale data sets has the potential of answering the most difficult and intriguing questions for evolutionary histories. However, such perspectives come with a higher complexity and difficulties for the phylogenomic inference. The focus of this thesis is exploring and providing insights into some of the questions arisen from theory, algorithms and applications of phylogenomics. The main contributions of the thesis deal with phylogenetic terraces, which represent sets of species trees in tree space with identical score (likelihood or parsimony). Firstly, we provide the rules to detect terraces during the tree search. To this end we study the induced partition trees and how topological rearrangements on species tree drive changes on partition trees. If the tree rearrangement operation applied to the current species tree does not change any of its associated induced partition trees, then the current and a new species trees belong to one terrace. We proof three propositions defining the rules when Nearest Neighbour Interchange (NNI), Subtree Pruning and Regrafting (SPR) and Tree Bisection and Reconnection (TBR) operations change the induced partition trees. We further generalize the concept of terraces to partial terraces and study their occurrence for real alignments using NNI neighbourhoods. Secondly, we provide a phylogenetic terrace aware data structure (PTA) for the efficient analysis of concatenated multiple alignments. Using PTA and the rules developed to detect (partial) terraces in the presence of missing data one saves computational time by avoiding unnecessary recomputations. We implemented PTA in IQ-TREE and tested its performance on 11 real alignments. Identification of partial terraces speeded up the tree search with IQ-TREE for up to 5 and 6 times compared to the standard implementation (terrace-unaware) and RAxML, respectively. PTA is suitable for the use with all partition models and all common topological rearrangement operations, such as NNI, SPR and TBR. Finally, we develop methods for conservation biology and ecology, where phylogenomics is used to quantify the evolutionary diversity of the species. We discuss the viable taxon selection problem, which incorporates predator-prey interactions to define viability constraints. First, we extend the problem to account for Split Diversity (SD), a biodiversity measure, which is based on the evolutionary distances between species on split networks. Second, to make the viability constraints more realistic we extend the viability definition to account for the diet composition of predators. SD with the viability constraints is used to prioritize species for the conservation actions. Though such optimization problems fall into the area of NP-hard problems, it is possible to solve them within reasonable amount of time using Integer Linear Programming (ILP), a well-known method for the decision-making problems. We provide the ILP formulations for all the discussed problems and implement them in the PDA software package. To exemplify the discussed methods we apply them to a real case study – the Caribbean Coral Reef community

Теоретичні засади, стан і практика розвитку платіжних систем в Україні

In modern conditions payment systems have an important role in the economy, as they must provide effective economic means of payments. Accordingly, the development of payment systems in Ukraine appears as a relevant theoretical and practical problem.In the article the theoretical basis and features of payment systems in Ukraine were researched. Preconditions of systemically important payment systems development been analyzed, which are performed by the key principles of their organization and functioning. Realization of principles of systemically important payment systems in Ukraine was investigated. The key principles of operation and functioning and their implementation in retail payment systems were determining, such as providing competitive services, security payments from outside interference, territorial and temporal availability, profitability of participation in the payment system, consumer protection, instant calculation of account balance, instant currency conversion and minimize currency risk.Recommendations for improving the procedures for conversion of currencies in the international card payment systems were provided in order to reduce currency risks for end-users and issuing banks, such as introducing restrictions on the period of submission for payment of international trade, as well prohibit use of trade-service enterprises for currency conversion their own exchange rates. The necessity of legislative regulation of the size of interchange fee in card payment systems to create more favorable conditions for the spread of retail electronic payment was determined as well as removal of legal restrictions on the issuance and use of electronic money and foreign exchange restrictions in order to create the conditions for international payment systems based on electronic money to enter the Ukrainian payment market.Статья посвящена исследованию теоретических основ платежных систем в Украине. Показано, что предпосылки развития основных платежных систем заключаются в соблюдении ключевых принципов их организации и функционирования. Определены особенности развития платежных систем в Украине.Даны рекомендации по совершенствованию процедур конвертации валют в международных карточных платежных системах. Установлена необходимость законодательного регулирования размера межбанковских комиссий в карточных платежных системах и снятия законодательных ограничений на эмиссию и использование электронных денег.У статті досліджено теоретичні основи розвитку платіжних систем в Україні. Показано, що передумови розвитку основних платіжних систем полягають у виконанні ключових принципів їх організації та функціонування. Визначено особливості розвитку платіжних систем в Україні.Надано рекомендації щодо вдосконалення процедур конвертації валют у міжнародних карткових платіжних системах. Встановлена необхідність законодавчого регулювання розміру міжбанківських комісій у карткових платіжних системах і зняття законодавчих обмежень на емісію та використання електронних грошей

Online-Appendix-Chernomor_et_al

Online-Appendix-Chernomor_et_a

Data from: Terrace aware data structure for phylogenomic inference from supermatrices

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Though partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software