Guide to Tree Files (Supplemental C): stage1 Polypodium_St170id.trees: Contains all genetrees generated from stage 1 used for concordance mapping Polypodium_St170id_ML.tre: Maximum likelihood tree inferred with RAxML based on the concatenated dataset from stage 1. St1_cfmap_ML.cf.tree: Stage 1 maximum Likelihood tree with concordance factors calculated by IQTREE. Polypodium_St170id.nex: Stage 1 alignment in nexus format. Polypodium_St170id_partitions.txt: Stage 1 partition file for alignment of generated loci. stage2 Polypodium_St270id_phased.trees: Contains all genetrees generated from stage 2 used for ASTRAL tree inference and concordance mapping Polypodium_St270id_ML.tre: Maximum likelihood tree inferred with RAxML based on the concatenated dataset from stage 2. Polypodium_st270id_ASTRAL.tre: Multi-species Coalescent tree inferred with ASTRAL based on genetrees from stage 2. Polypodium_St2_ML.cf.tree: Stage 2 maximum likelihood tree with concordance factors calculated by IQTREE. Polypodium_st270id_ASTRAL.cf.tree: Stage 2 multi-species Coalescent tree with concordance factors calculated by IQTREE. Polypodium_st270id_phased.nex: Stage 2 alignment in nexus format. Polypodium_st270id_phased_partitions.txt: Stage 2 partition file for alignment of generated loci. stage3 Each folder here corresponds to the allotetraploid samples we studied with stage 3 of the pipeline. sampleid_70id.trees: Contains all genetrees generated from stage 3 used for ASTRAL tree inference and concordance mapping sampleid_collapsed_70id_ML.tre: Final maximum likelihood tree inferred with RAxML based on the concatenated dataset from stage 3. sampleid_70id_ASTRAL.tre: Multi-species Coalescent tree inferred with ASTRAL based on genetrees from stage 3 and collapsed haplotype tips from the final maximum likelihood tree. sampleid_ASTRAL_cfmap.cf.tree: Stage 3 multi-species Coalescent tree with concordance factors calculated by IQTREE. sampleid_70id.phy: Stage 3 alignment in phylip format. sampleid_70id_partitions.txt: Stage 3 partition file for alignment of generated loci. Guide to Sensitivity Analysis Files (Supplemental D): *id_50rep.tre : Maximum likelihood trees generated at 50% through 80% identity clustering of consensus alleles mapping to the same reference locus at 5% intervals. Loci had to have 50% sample representation in order to be included in analysis. *id_50rep.phy : Phylip alignments corresponding to 50% through 80% identity clustering of consensus alleles mapping to the same reference locus at 5% intervals. Polypodium_unclustered_ML_50rep.tre : Maximum likelihood tree for the unclustered (i.e 0% clustering) consensus alleles per reference locus at 50% sample representation. Polypodium_unclustered.phy : Phylip alignment for the unclustered (i.e. 0% clustering) consensus allele dataset at 50% sample representation. consensusalleles_clusterid*_SUMMARY_TABLE.csv : Set of matrices showing the number of consensus-alleles per locus per sample at 50% through 80% identity clustering thresholds. consensusalleles_c199_contig_csl300_csn9.csv : Matrix showing the number of consensus-alleles per locus per sample in the unclustered dataset.