Supplementary material for: Phylogenetic analysis of allotetraploid species using polarized genomic sequences
Creators: name: Leal, J. L.
name: Milesi, Pascal
name: Salojärvi, Jarkko
name: Lascoux, Martin
Publisher: name: Zenodo
Year: 2022
Subjects: allopolyploidy
Arabidopsis
genomic polarization
homoeologs
incomplete lineage sorting
Phasing
polyploid phylogenetics
reticulate evolution

description: Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing – to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid – while vastly simplifying its implementation by reducing a complex multi-stage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods – usually an expensive, complex, and/or time-consuming endeavor – phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization which, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read as well as short-read high-throughput sequencing (HTS) data, and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS), and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of <em>Arabidopsis kamchatica</em> and <em>A. suecica</em>, two allopolyploids whose ancestry has been well documented.
description: General Description A. Arabidopsis_Data.tzr.gz: Contains data used in Arabidopsis case study (used to produce Fig. 3, Fig. 4, Fig. S2, Fig. S3, Fig. S4 and Fig. S5). B. SIMULATIONS.tzr.gz: Contains simulation results for moderate and high ILS scenarios (used to produce Fig. 2). C. SIMULATIONS_No-ILS-No-polytomy.tzr.gz: Contains simulation results for the "No-ILS-No-polytomy" scenario (used to produce Fig. 2). Detailed description Note: Description of the pipeline used, including scripts, is available at: https://github.com/LLN273/Genomic_polarization_allotetraploids Please see the provided README for more details about using and viewing these files. Funding provided by: Svenska Forskningsrådet Formas<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001862<br>Award Number: 2016-00780Funding provided by: Svenska Forskningsrådet Formas<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001862<br>Award Number: 2020-01456
description: Analysis based on publicly available sequencing data, available in The European Nucleotide Archive (ENA) at www.ebi.ac.uk, under PRJNA284572, PRJNA273563, and PRJEB14544 accession codes.