DOI: 10.5061/dryad.2547d7wxq
title: Data from: The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae

description: Premise: Hybridization is recognized as an important mechanism in fern
 speciation, with many well-studied examples of allopolyploids forming
 among congeners, as well as evidence of ancient genome duplications.
 Several contemporary instances of deep (intergeneric) hybridization have
 been noted, invariably resulting in sterile progeny. We chose the
 christelloid lineage of the family Thelypteridaceae to investigate recent
 hybridization between deeply diverged lineages among extant taxa. We also
 seek to understand the ecological and evolutionary outcomes of resulting
 lineages across the landscape. Methods: By phasing captured reads within a
 phylogenomic dataset of GoFlag 408 nuclear loci using HybPhaser, we
 investigated candidate hybrids to identify parental lineages within the
 christelloid clade. We estimated divergence ages by inferring a dated
 phylogeny using fossil calibrations with treePL. We investigated
 ecological niche conservatism between one confirmed intergeneric
 allotetraploid and its diploid progenitors using the centroid, overlap,
 unfilling, and expansion (COUE) framework, based on PCA. Key Results: We
 provide evidence for at least six instances of intergeneric hybrid
 speciation within the christelloid clade, and estimate up to 45 million
 years of divergence between progenitors. The niche quantification analysis
 showed moderate niche overlap between an allopolyploid species and its
 progenitors, with significant divergence from the niche of one progenitor
 and conservatism to the other. Conclusions: The examples provided here
 highlight the overlooked role that allopolyploidization following
 intergeneric hybridization may play in fern diversification and range and
 niche expansions. Applying this approach to other fern taxa may reveal a
 similar pattern of deep hybridization resulting in highly successful novel
 lineages.
description: Please refer to the methods section of the associated publication
 for a detailed description of datasets and analyses.
description: # The role of deep hybridization in fern speciation: Examples from the
 Thelypteridaceae
 [https://doi.org/10.5061/dryad.2547d7wxq](https://doi.org/10.5061/dryad.2547d7wxq) This dataset includes all supplementary information associated with Tseng, Kuo, Borokini and Fawcett (submitted to the American Journal of Botany). Previously published sequence data are available on Dryad [doi.org/10.5061/dryad.gxd2547j4](https://doi.org/10.5061/dryad.gxd2547j4) (Fawcett et al. 2022) and NCBI Sequence Read Archive Bioproject 646399. Appendix S1. List of voucher specimens used in phylogenetic analyses, including associated data. This is a subset of the samples used in Fawcett et al. 2021.    Appendix S2. Scatterplot representing the locus heterozygosity (LC) and allele divergence (AD) across the samples. Each data point corresponds to an individual sample, with two categories indicated by labels: "Phased sample (H)" and "Clade reference (R)". The plot was generated using HybPhaser.   Appendix S3. Phylogenetic tree of christelloid clade reconstructed using maximum likelihood analysis based on GoFlag 408 loci sequence data. Major clades within the tree are designated as Clade A to Clade H. Clade references are denoted by blue colors. Numbers above branches indicate bootstrap values of maximum likelihood  (MLBS)/gene concordance factors (gCF) / site concordance factor (sCF).   Appendix S4 Divergence estimates and partition models used in dating analysis.   Appendix S6 Heat Map showing sequence recovery.   Appendix S5 Georeferenced specimens used for niche analysis.   Appendix S6 Heat map showing recovery efficiency for 451 GoFlag loci in the christelloid clade, assembled by HybPiper. Columns represent loci and rows are samples. Colors indicate sequence recovery percentage relative to reference gene length.   Appendix S7 Table. Sequence length, AD, LH and result of percentages of reads matching to each reference in our sampling. Clade reference and phased sample are noted. Red highlights indicate higher percentages of unambiguous read mappings to the reference in phased samples.