DOI: 10.5061/dryad.1c59zw3xc
title: Data from: Phylogenomic structure and speciation in an emerging model: The Sphagnum magellanicum complex (Bryophyta)

description: The moss genus Sphagnum has unparalleled ecological importance because
 some 30% of the total terrestrial carbon pool is bound up in
 Sphagnum-dominated peatlands. A major peat-former, S. magellanicum, is one
 of two species for which a reference-quality genome exists to facilitate
 research in ecological genomics, but recently published work indicated
 that S. magellanicum s. str. is restricted to South America and two other
 species, S. divinum and S. medium occur in North America and Europe. We
 report herein that there are four clades/species within the S.
 magellanicum complex in eastern North America, two in South America, and
 another in eastern Asia. The reference genome belongs to S. divinum.
 Phylogenetic analyses at the whole genome and chromosome levels, using
 genome resequencing and RADseq, resolve sister group relationships within
 the complex. Species are monophyletic in most analyses and exhibit tens of
 thousands (RADseq) to millions (resequencing) of fixed nucleotide
 differences, but two, referred to informally as S. diabolicum and S. magni
 because they have not been formally described, are differentiated by only
 hundreds (RADseq) to thousands (resequencing) of differences. Data from 14
 of the 19 resequenced chromosomes (7 chromosomes for RADseq) resolve the
 reciprocal monophyly of S. magni and S. diabolicum. These two appear to be
 in the process of speciation and because they differ in geographic ranges
 and the climate zones they occupy – S. diabolicum in boreal peatlands and
 S. magni in warm temperate to subtropical communities of the southern U.S.
 – they provide an exciting opportunity for comparative genomic analyses of
 climate niche evolution. Introgression among species in the complex is
 demonstrated using D-statistics and f4-ratios. One ecologically important
 functional trait that underlies peat (carbon) accumulation, tissue
 decomposability, does not differ between segregate North American species
 in the S. magellanicum complex although previous research showed that many
 related Sphagnum species have evolved differences in
 decomposability/carbon sequestration. Phylogenetic resolution and more
 accurate species delimitation in the S. magellanicum complex substantially
 increase the value of this group for studying the early evolutionary
 stages of climate adaptation, and ecological evolution more broadly.
description: <strong>RADseq data</strong>: 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 with 150bp
 single-ended reads.
 <strong>"RADseq-like" in silico digested genomic
 data</strong>: 43 genomic resequencing assemblies were digested
 <em>in silico</em> 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 number
 of 10 copies (enough to pass downstream depth filters).
 <strong>Chloroplast alignment</strong>: Plastid reads
 from 49 resequenced genomes were identified and assembled into contigs
 using NOVOPlasty. For each genome, contigs were manually aligned to the
 published <em>Sphagnum palustre</em> plastid genome (KU726621)
 and to each other to identify the Inverted Repeat boundaries and generate
 a single incomplete plastid genome sequence (with missing data represented
 by strings of Ns). Each sequence includes the Long Single Copy region, one
 copy of the Inverted Repeat, and the Small Single Copy region. Sequences
 were aligned with MAFFT. Further details on processing
 methods are available in the associated manuscript.
description: <strong>File chloroplast_alignment.mafft.gz</strong>:
 Zipped fasta format file with an alignment of 49 chloroplast genomes (the
 Long Single Copy Region, Inverted Repeat, and Small Single copy
 region--the second copy of the inverted repeat is omitted).
 <strong>File
 demultiplexed_sample_data-radseq.tar.gz</strong>: Zipped folder with
 149 files of demultiplexed fastq format Illumina reads from RADseq
 samples. <strong>File
 demultiplexed_sample_data-insilico.tar.gz</strong>: Zipped folder
 with 43 files of fastq format "RADseq-like" reads from in silico
 digested genome resequencing samples.