Data from: Genetic structure of the Sphagnum magellanicum (Sphagnaceae) complex in Europe
Data files
Aug 27, 2025 version files 68.56 GB
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demultiplexed_reads-insilico.tar.gz
111.16 MB
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demultiplexed_reads-radseq1.tar.gz
7.78 GB
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demultiplexed_reads-radseq2.tar.gz
8.05 GB
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demultiplexed_reads-radseq3.tar.gz
8.38 GB
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demultiplexed_reads-radseq4.tar.gz
7.23 GB
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demultiplexed_reads-radseq5.tar.gz
9.14 GB
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demultiplexed_reads-radseq6.tar.gz
8.77 GB
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demultiplexed_reads-radseq7.tar.gz
9.23 GB
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demultiplexed_reads-radseq8.tar.gz
9.86 GB
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md5sum.txt
622 B
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README.md
5.48 KB
Abstract
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.
Principal Investigator/Corresponding author:
A. Jonathan Shaw, Duke University, shaw@duke.edu
Data prepared by:
Aaron M. Duffy, Duke University, 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.