Arthur Zwaenepoel

Arthur Zwaenepoel — PhD student
Joined the group in 2017

As a computational biologist in a broad sense, I currently direct my research efforts towards tackling questions in evolutionary biology by computational and statistical means. I am mainly working in the field of evolutionary genomics, where we try to understand the evolution of genomes by combining phylogenetics, molecular evolution and comparative genomics. Here I am focusing on the evolutionary importance of ancient whole genome duplications (in plants) and their inference from genome data.

I am strongly impressed by the power of stochastic models and (bayesian) statistics in science, and strive for fruitful applications thereof in my research. Additionally, I enjoy theoretical (eco-)evolutionary genetics, and I would like to study the interplay between evolutionary, ecological and demographic factors that might have led to an increased establishment of polyploid species during periods of environmental upheaval from a theoretical perspective. In general, I am intrigued, but also to some degree skeptical, about the possibility and fruitfulness of a 'theoretical biology'.

Perhaps the first lesson to be learned from biology is that there are lessons to be learned from biology. - Robert Rosen (2013), Essays on Life Itself

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Birth: February 20, 1995, Ghent (Belgium)

Education

September 2012 - June 2015: Bachelor of Science in Biochemistry & Biotechnology, Ghent University
September 2013 - June 2015: Honours programme: Quetelet Colleges, Ghent University
September 2015 - June 2017: Master of Science in Bioinformatics (Systems Biology), Ghent University

Publications

  1. Zwaenepoel, A., & Van de Peer, Y. (2020). Model-based detection of whole-genome duplications in a phylogeny. MOLECULAR BIOLOGY AND EVOLUTION, 37(9), 2734–2746. https://doi.org/10.1093/molbev/msaa111
    Ancient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection of ancient WGDs in a phylogenetic context have two main drawbacks. The first is that unwarranted restrictive assumptions on the ‘background’ gene duplication and loss rates make inferences unreliable in the face of model violations. The second is that most methods can only be used to examine a limited set of a priori selected WGD hypotheses; and cannot be used to discover WGDs in a phylogeny. In this study we develop an approach for WGD inference using gene count data that seeks to overcome both issues. We employ a phylogenetic birth-death model that includes WGD in a flexible hierarchical Bayesian approach, and use reversible-jump MCMC to perform Bayesian inference of branch-specific duplication, loss and WGD retention rates accross the space of WGD configurations. We evaluate the proposed method using simulations, apply it to data sets from flowering plants and discuss the statistical intricacies of model-based WGD inference.
  2. Roelofs, D., Zwaenepoel, A., Sistermans, T., Nap, J., Kampfraath, A. A., Van de Peer, Y., … Kraaijeveld, K. (2020). Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution. BMC BIOLOGY, 18(1). https://doi.org/10.1186/s12915-020-00789-1
    Background: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. Results: Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (KS), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs. Conclusions: Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.
  3. Zhang, J., Fu, X.-X., Li, R.-Q., Zhao, X., Liu, Y., Li, M.-H., … Chen, Z.-D. (2020). The hornwort genome and early land plant evolution. NATURE PLANTS, 6(2), 107–118. https://doi.org/10.1038/s41477-019-0588-4
    Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
  4. Zwaenepoel, A., & Van de Peer, Y. (2019). wgd-simple command line tools for the analysis of ancient whole genome duplications. BIOINFORMATICS, 35(12), 2153–2155.
    MOTIVATION: Ancient whole genome duplications (WGDs) have been uncovered in almost all major lineages of life on Earth and the search for traces or remnants of such events has become standard practice in most genome analyses. This is especially true for plants, where ancient WGDs are abundant. Common approaches to find evidence for ancient WGDs include the construction of KS distributions and the analysis of intragenomic co-linearity. Despite the increased interest in WGDs and the acknowledgement of their evolutionary importance, user-friendly and comprehensive tools for their analysis are lacking. Here, we present an easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and co-linearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner. AVAILABILITY & IMPLEMENTATION: wgd is free and open source software implemented in Python and is available at https://github.com/arzwa/wgd. SUPPLEMENTARY INFORMATION: Supplementary methods are available at Bioinformatics online.
  5. Zwaenepoel, A., Li, Z., Lohaus, R., & Van de Peer, Y. (2019). Finding evidence for whole genome duplications : a reappraisal. MOLECULAR PLANT, 12(2), 133–136.
  6. Zwaenepoel, A., & Van de Peer, Y. (2019). Inference of ancient whole-genome duplications and the evolution of gene duplication and loss rates. MOLECULAR BIOLOGY AND EVOLUTION, 36(7), 1384–1404.
    Gene tree - species tree reconciliation methods have been employed for studying ancient whole genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rate across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigate the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.
  7. Zwaenepoel, Arthur, Diels, T., Amar, D., Van Parys, T., Shamir, R., Van de Peer, Y., & Tzfadia, O. (2018). MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants. FRONTIERS IN PLANT SCIENCE, 9.
    Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named "MORPH bulk" (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest.