DOI: 10.5061/dryad.dfn2z353j
title: Supplementary material for: Phylogenetic analysis of allotetraploid species using polarized genomic sequences

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 Arabidopsis kamchatica
 and A. suecica, two allopolyploids whose ancestry has been well
 documented.
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.
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.