Complex polyploids: Origins, genomic composition, and role of introgressed alleles

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploid, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an ..., Analysis based on 269 newly sequenced B. pubescens individuals collected from twenty-tree locations along the species' range. Additional accessions were obtained from the European Nucleotide Archive (ENA) for B. lenta, B. nana, B. occidentalis, B. pendula, B. platyphylla, B. populifolia, B. pubescens, Alnus glutinosa, and A. incana, at www.ebi.ac.uk, under the PRJEB14544 accession code. For the newly collected samples, individual libraries were generated using custom probes designed for targeted exome capture and sequenced on paired-end mode (150 bp) on an Illumina NovaSeq 6000 platform., , # Supplementary data for: Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles
#### J.L. Leal, Pascal Milesi, Eva Hodková, Qiujie Zhou, Jennifer James, D. Magnus Eklund, Tanja Pyhäjärvi, Jarkko Salojärvi, and Martin Lascoux
#### https://doi.org/10.5061/dryad.5tb2rbp9f
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Scripts used for analysis of complex polyploids are available at:
https://github.com/LLN273/Complex-Polyploids

## General description

**A. Analysis of B. pubescens genomic data**

Data used to produce Fig. 2a, Fig. 2b, Fig. S7, and Fig. S8.
01_MSAs_BEFORE_POLARIZATION.tzr.gz
02_MSAs_AFTER_POLARIZATION.tzr.gz
03_IQTREE_RESULTS.tzr.gz
04_Polyploid_pairing_profiles.tzr.gz

**B. STRUCTURE analysis:**

Results from STRUCTURE analysis (used to produce Fig. 2c, Fig. S9, and Fig. S10).
05_STRUCTURE_analysis.tzr.gz

**C. DAPC analysis:**

Input data used to produce Fig. 2d, and Fig. S11.
06_DAPC_adegenet_analysis.tzr.gz

**D. Simulated datasets and polyploidization model te...