DOI: 10.5061/dryad.bzkh189mp
title: Data from: Genetic structure of the Sphagnum magellanicum (Sphagnaceae) complex in Europe

description: Sphagnum magellanicum has historically been interpreted as a widespread
 species across both the Northern and Southern Hemispheres. Recent
 research, however, indicates that it comprises at least seven phylogenetic
 species, and that S. magellanicum s.str. It is restricted to southern
 Argentina and Chile. Four species are recorded from North America, and two
 of them, S. divinum and S. medium, are known to occur in Europe
 (and are typified by European collections). Here, we assess European
 plants of this complex to test if two apparent North American endemics, S.
 diabolicum and S. magniae, occur in Europe, and document the genetic
 structure of European species of the complex, including gametophyte sex
 ratios and patterns of genetic diversity. We further assess evidence for
 gene flow between the species in Europe and between North American and
 European plants of species that occur on both continents. Molecular data,
 especially RADseq, were used to assess genetic and phylogenetic patterns,
 and additional plants were identified with barcode markers to document
 European geographic distributions. The results indicate that S. diabolicum
 and S. magniae are endemic to North America. In Europe, S. divinum is more
 genetically diverse than S. medium. Sex ratios in both species did not
 depart from 50:50. Low levels of interspecific gene flow between the two
 species occur in Europe, as well as higher levels of gene flow between
 North American and European plants within S. divinum and S. medium.
 Overall, our results corroborate evidence that S. divinum and S. medium
 are phylogenetically distinct species and represent separate gene pools
 despite low levels of introgression.
description: # Data from: Genetic structure of the *Sphagnum magellanicum*
 (Sphagnaceae) complex in Europe 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:  Marta Nieto-Lugilde, Duke University Blanka Aguero,
 Duke University; Robinson, SUNY Oneonta Kristian Hassel, Norwegian
 University of Science and Technology Kjell Ivar Flatberg, Norwegian
 University of Science and Technology; Ingerpuu, University of Tartu Kai
 Vellak, University of Tartu Aaron Pérez-Haase, Universitat de Barcelona
 Martin Jiroušek, Mendel University in Brno Mathias Krebs, Universität
 Greifswald Teemu Juselius-Rajamäki, University of Helsinki Sanna Piilo,
 University of Helsinki Bjorn Robroek, Radboud University Nijmegen Paul
 Lamkowski, Universität Greifswald Gustaf Granath, Uppsala University Date
 collected: 2019-2024 These datasets contain DNA sequences for *Sphagnum
 magellanicum* group plants collected from the following countries: 
 Austria, Czech Republic, Denmark, Estonia, Finland, France, Germany,
 Iceland, Ireland, Latvia, Lithuania, Norway, Poland, Russia, Spain,
 Sweden, Switzerland, The Netherlands, Canada (Alberta, British Columbia,
 Labrador, Newfoundland, Quebec), USA (Alabama, Arkansas, Florida, Georgia,
 Maine, Michigan, Minnesota, New Hampshire, New Jersey, New York, North
 Carolina, Pennsylvania, Vermont, Washington, West Virginia, Wisconsin).
 Collection locations for specific samples included in this dataset can be
 found in Table S1 of the associated manuscript. **RADseq data**: Genomic
 DNA was extracted from a single capitulum of each herbarium sample or new
 collection. RADseq libraries were prepared following a double-digestion
 restriction site-associated DNA sequencing (ddRADseq) protocol. Each
 library was sequenced on a single lane of Illumina NextSeq 500 or NovaSeq
 6000 with 150bp single-ended reads or HiSeq 2000 with 100bp single-ended
 reads. **"RADseq-like" in silico digested genomic data**:
 Genomic resequencing assemblies were digested in silico with EcoRI and
 MseI using the program “restrict” from the EMBOSS package. Custom scripts
 were used to filter for digested sequence fragments with an EcoRI cutsite
 at one end and an MseI cutsite at the other, to mimic the size-selection
 steps of a RADseq library preparation, to trim the fragments to match the
 length of our quality-filtered Illumina reads, and to write the sequences
 to a FASTQ-formatted file. Each resulting “read” was given a quality score
 of all "E" (high enough to pass downstream quality filters and
 several 10 copies (enough to pass downstream depth filters). #### Data and
 file overview: * demultiplexed_reads-radseq1.tar.gz: This zipped folder
 contains zipped fastq format Illumina reads from 30 *Sphagnum* RADseq
 samples. The reads are untrimmed but have been demultiplexed with one
 sample per file. File names match the sample name. -
 demultiplexed_reads-radseq2.tar.gz: This zipped folder contains zipped
 fastq format Illumina reads from 30 *Sphagnum* RADseq samples. The reads
 are untrimmed but have been demultiplexed with one sample per file. File
 names match the sample name. * demultiplexed_reads-radseq3.tar.gz: This
 zipped folder contains zipped fastq format Illumina reads from 30
 *Sphagnum* RADseq samples. The reads are untrimmed but have been
 demultiplexed with one sample per file. File names match the sample name.
 - demultiplexed_reads-radseq4.tar.gz: This zipped folder contains zipped
 fastq format Illumina reads from 30 *Sphagnum* RADseq samples. The reads
 are untrimmed but have been demultiplexed with one sample per file. File
 names match the sample name. * demultiplexed_reads-radseq5.tar.gz: This
 zipped folder contains zipped fastq format Illumina reads from 30
 *Sphagnum* RADseq samples. The reads are untrimmed but have been
 demultiplexed with one sample per file. File names match the sample name.
 - demultiplexed_reads-radseq6.tar.gz: This zipped folder contains zipped
 fastq format Illumina reads from 30 *Sphagnum* RADseq samples. The reads
 are untrimmed but have been demultiplexed with one sample per file. File
 names match the sample name. * demultiplexed_reads-radseq7.tar.gz: This
 zipped folder contains zipped fastq format Illumina reads from 30
 *Sphagnum* RADseq samples. The reads are untrimmed but have been
 demultiplexed with one sample per file. File names match the sample name.
 - demultiplexed_reads-radseq8.tar.gz: This zipped folder contains zipped
 fastq format Illumina reads from 30 *Sphagnum* RADseq samples. The reads
 are untrimmed but have been demultiplexed with one sample per file. File
 names match the sample name. - demultiplexed_reads-insilico.tar.gz: This
 zipped folder contains zipped fastq format "RADseq-like" reads
 from 16 in silico digested genome resequencing samples. These are not
 actually Illumina reads, but are the result of *in silico* digesting and
 processing 16 resequenced genomes to generate the equivalent of Illumina
 RADseq reads, which allows resequenced genome samples to be included in
 RADseq analyses. 10 copies of each read (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. * md5sum.txt: Text file containing MD5 checksum
 values for each of the data files.