DOI: 10.5061/dryad.mgqnk99bn
title: Data from: Climate niches structure a regional hybrid zone in <em>Sphagnum</em> (peatmoss, Bryophyta)

description: Premise: Hybridization is an important evolutionary process across all
 groups of embryophyte land plants, but relatively little is known about
 hybridization and introgression in spore producing plants with a dominant
 gametophyte life cycle stage (i.e., bryophytes). The Sphagnum magellanicum
 complex, with four North American species, is proving to be a valuable
 system for studying population genomics, speciation, and climate
 adaptation. This paper focuses on hybridization between the four species,
 with focus on a regional zone where virtually all plants in the two most
 recently diverged species (S. diabolicum, S. magniae) show genetic
 admixture. Methods: Analyses of population genetics and introgression
 utilized three types of molecular data: RADseq, “RADseq-like” data derived
 from in silico digestion of genome sequences, and species-specific barcode
 markers developed previously for this group. 582 gametophytes were sampled
 from 79 collecting sites representing 23 U.S. states and five Canadian
 provinces, from 27 o to 56o N. A range of analytical methods were
 employed: phylogeny reconstruction, STRUCTURE to assess individual genetic
 admixture, demographic modeling to estimate the timing and extent of
 interspecific gene flow, and comparative genomics to evaluate the
 occurrence and locations of introgressed SNPs. Results: Low but
 significant gene flow was detected among all pairwise combinations of
 extant species as well as between ancestral lineages and those species.
 Greater genetic similarities among species where they occur sympatrically
 within peatlands suggests that hybridization is on-going. Hybridization
 between S. diabolicum and S. magniae is especially pronounced and plants
 in a regional zone from North Carolina to New Jersey are genetically
 admixed. Demographic analyses all indicate that this admixture reflects
 hybridization, not just incomplete lineage sorting. Introgressed SNPs were
 detected across all chromosomes but introgressed SNPs fixed in genetically
 pure samples of the two species were concentrated on four autosomes: 2, 7,
 14, and 19. Introgression block sizes and numbers were positively
 correlated with the level of genetic admixture. Patterns of genomic
 admixture/introgression were significantly correlated with climate
 variation across collection sites within the hybrid zone. Conclusions:
 Previous analyses indicated that climate adaptation has played an
 important role in speciation within this group, especially the divergence
 of warm-temperate to subtropical S. magniae from cold-temperate to boreal
 S. diabolicum. This work shows that the genomic structure of plants in a
 regional hybrid zone between S. magniae and S. diabolicum is also
 structured by climate adaptation and strengthens the value of this group
 for learning more about both speciation and climate adaptation.
description: # Data from: Climate niches structure a regional hybrid zone in *Sphagnum*
 (peatmoss, Bryophyta)
 [https://doi.org/10.5061/dryad.mgqnk99bn](https://doi.org/10.5061/dryad.mgqnk99bn) Principal Investigator/Corresponding author: A. Jonathan Shaw, Duke University, [shaw@duke.edu](mailto:shaw@duke.edu) Data prepared by: Aaron M. Duffy, Duke University, [aduffy70@gmail.com](mailto:aduffy70@gmail.com) Co-investigators: Blanka Aguero, Duke University Marta Nieto-Lugilde, Duke University Karn Imwattana, Chulalongkorn University Sean Robinson, SUNY Oneonta Scott Schuette, Western Pennsylvania Conservancy Richard Wilkens, Salisbury University Joseph Yavitt, Cornell University David J. Weston, Oak Ridge National Laboratory Brian Piatkowski, Mayo Clinic Gustaf Granath, Uppsala University Date collected: 2021-2024 These datasets DNA sequences for *Sphagnum magellanicum* group plants collected from the U.S. states of North Carolina and Georgia. Collection locations for specific samples included in this dataset can be found in Appendix S1 of the associated manuscript. Data for samples included in the associated manuscript that are not included in this dataset are available in the Dryad Digital Repository at [https://doi.org/10.5061/dryad.37pvmcvtk](https://doi.org/10.5061/dryad.37pvmcvtk) Funding: U.S. National Science Foundation, Award: DEB-1737899 U.S. National Science Foundation, Award: DEB-1928514 Swedish Research Council, Award: 2018-04872 Carl Tryggers Foundation Vidfelts Foundation, Award: 2019-056 ## Data and file overview: demultiplexed_reads.tar.gz: This zipped folder contains zipped fastq format Illumina reads from 6 *Sphagnum* RADseq samples. The reads are untrimmed but have been demultiplexed with one sample per file. File names match the sample name. 2025-07-29 demultiplexed_reads-insilico.tar.gz: This zipped folder contains zipped fastq format "RADseq-like" reads from 9 *in silico* digested genome resequencing samples. These are not actually Illumina reads, but are the result of *in silico* digesting and processing 9 resequenced genomes to generate the equivalent of Illumina RADseq reads, which allows resequenced genome samples to be included in RADseq analyses. Ten copies of each read are included (enough to pass downstream depth filters) with quality values all set to "E" (high enough to pass quality filters in RADseq assembly software such as ipyrad). File names match the sample name. 2025-09-17 md5sum.txt: Text file containing md5 checksum values for each of the datafiles. 2025-09-17