Supplementary material for: Phylogenetic analysis of allotetraploid species using polarized genomic sequences

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 ..., 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. , 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.Â

多倍体杂交物种的系统发育分析长期以来都是一项严峻挑战，因为其需要区分不同祖先起源的等位基因，方能厘清其各自的演化历史。此前已有研究将系统发育视作网状网络，采用两步分型策略：首先识别并分离同源异型基因座（homoeologous loci），随后在第二步分型中将每个基因拷贝分配至异源多倍体物种的某一亚基因组。本文提出一种替代方案，该方案保留了分型方法的核心思想——生成能够捕捉多倍体网状演化历史的独立核苷酸序列，同时将复杂的多阶段流程简化为单一步骤，极大降低了实现难度。当前多数用于多倍体物种系统发育重建的现有方法，均需要通过实验或其他方式对测序读段进行预先分型……

本研究基于公开可得的测序数据开展分析，相关数据可在欧洲核苷酸档案库（European Nucleotide Archive, ENA，网址www.ebi.ac.uk）中通过登录号PRJNA284572、PRJNA273563及PRJEB14544获取。

通用说明
A. Arabidopsis_Data.tzr.gz：包含拟南芥案例研究所用数据集（用于生成图3、图4、图S2、图S3、图S4及图S5）。
B. SIMULATIONS.tzr.gz：包含中等及高强度不完全谱系分选（Incomplete Lineage Sorting, ILS）场景下的模拟结果（用于生成图2）。
C. SIMULATIONS_No-ILS-No-polytomy.tzr.gz：包含“无ILS无多歧分支”场景下的模拟结果（用于生成图2）。

详细说明
注：本研究所用分析流程（含相关脚本）的说明文档可访问：https://github.com/LLN273/Genomic_polarization_allotetraploids
如需了解文件使用与查看的更多细节，请参阅附带的README文件。