Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

Abstract Summary Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree—species tree reconciliations. Availability and implementation Source code and manual are freely available in https://github.com/AADavin/ZOMBI/. Supplementary information Supplementary data are available at Bioinformatics online.

[1]  J. Peter Gogarten,et al.  Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

[2]  D. Kendall.  On the Generalized "Birth-and-Death" Process , 1948 .

[3]  Sophie S Abby,et al.  Lateral gene transfer as a support for the tree of life , 2012, Proceedings of the National Academy of Sciences.

[4]  G. Fournier,et al.  Horizontal gene transfer constrains the timing of methanogen evolution , 2018, Nature Ecology & Evolution.

[5]  Stephanie J. Spielman,et al.  Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies , 2015, bioRxiv.

[6]  Joel Sjöstrand,et al.  GenPhyloData: realistic simulation of gene family evolution , 2013, BMC Bioinformatics.

[7]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[8]  Bastien Boussau,et al.  Gene transfers can date the Tree of Life , 2018, Nature Ecology & Evolution.

[9]  Gergely J. Szöllősi,et al.  Lateral Gene Transfer from the Dead , 2012, Systematic biology.

[10]  Robert G. Beiko,et al.  A simulation test bed for hypotheses of genome evolution , 2007, Bioinform..

[11]  David Posada,et al.  SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees , 2015, bioRxiv.

[12]  Soumya Kundu,et al.  SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution , 2019, Bioinform..

[13]  J. Gogarten,et al.  Cladogenesis, coalescence and the evolution of the three domains of life. , 2004, Trends in genetics : TIG.

[14]  L. Wilkinson.  BACTERIA , 1952, The Lancet.

[15]  G. Gonnet,et al.  ALF—A Simulation Framework for Genome Evolution , 2011, Molecular biology and evolution.

[16]  Sophie S Abby,et al.  Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations , 2012, Proceedings of the National Academy of Sciences.

[17]  V. Daubin,et al.  The pattern and process of gene family evolution , 2011, 1102.2331.

[18]  Andrew D. S. Cameron,et al.  Horizontal transfer of antibiotic resistance genes in clinical environments. , 2019, Canadian journal of microbiology.

[19]  H. Ochman,et al.  Lateral gene transfer and the nature of bacterial innovation , 2000, Nature.

[20]  Tanja Stadler,et al.  Sampling trees from evolutionary models. , 2010, Systematic biology.

[21]  P. Bork,et al.  ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data , 2016, Molecular biology and evolution.

[22]  Antonio Carvajal-Rodríguez,et al.  Simulation of Genomes: A Review , 2008, Current genomics.

[23]  Carole Knibbe,et al.  Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation , 2016, Genome biology and evolution.

[24]  W. Reed,et al.  POWER-LAW DISTRIBUTIONS FROM EXPONENTIAL PROCESSES : AN EXPLANATION FOR THE OCCURRENCE OF LONG-TAILED DISTRIBUTIONS IN BIOLOGY AND ELSEWHERE , 2003 .

[25]  Gergely J. Szöllősi,et al.  Integrative modeling of gene and genome evolution roots the archaeal tree of life , 2017, Proceedings of the National Academy of Sciences.

[26]  Dietmar Plenz,et al.  powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions , 2013, PloS one.

[27]  Vincent Berry,et al.  RecPhyloXML: a format for reconciled gene trees , 2018, Bioinform..