DOI: 10.5061/dryad.2ngf1vhv5
title: Data from: Clonality, local population structure, and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex

description: Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with approximately
 300-500 species. The genus has unparalleled ecological importance because
 Sphagnum-dominated peatlands store almost a third of the terrestrial
 carbon pool, and peatmosses engineer the formation and microtopography of
 peatlands. Genomic resources for Sphagnum are being actively expanded, but
 many aspects of their biology are still poorly known. Among these are the
 degree to which Sphagnum species reproduce asexually, and the relative
 frequencies of male and female gametophytes in these haploid-dominant
 plants. We assess clonality and gametophyte sex ratios and test hypotheses
 about the local-scale distribution of clones and sexes in four North
 American species of the S. magellanicum complex. These four species are
 difficult to distinguish morphologically and are very closely related. We
 also assess microbial communities associated with Sphagnum host plant
 clones and sexes at two sites.  405 samples of the four species,
 representing 57 populations, were subjected to RADseq. Analyses of
 population structure and clonality based on the molecular data utilized
 both phylogenetic and phenetic approaches. Multi-locus genotypes (genets)
 were identified using the RADseq data. Sexes of sampled ramets were
 determined using a molecular approach that utilized coverage of loci on
 the sex chromosomes after the method was validated using a sample of
 plants that expressed sex phenotypically. Sex ratios were estimated for
 each species, and populations within species. Differences in fitness
 between genets were estimated as the number of ramets each genet
 comprised. Degree of clonality (numbers of genets/numbers of ramets
 [samples]) within species, among sites, and between gametophyte sexes were
 estimated. Sex ratios were estimated for each species, and populations
 within species. Sphagnum-associated microbial communities were assessed at
 two sites in relation to Sphagnum clonality and sex. All four species
 appear to engage in a mixture of sexual and asexual (clonal) reproduction.
 A single ramet represents most genets but 2-8 ramets were detected for
 some genets. Only one genet is represented by ramets in multiple
 populations; all other genets are restricted to a single population.
 Within populations ramets of individual genets are spatially clustered,
 suggesting limited dispersal even within peatlands. Sex ratios are
 male-biased in S. diabolicum but female-biased in the other three species,
 although significantly so only in S. divinum. Neither species nor
 males/females differ in levels of clonal propagation. At St. Regis Lake
 (NY) and Franklin Bog (VT), microbial community composition is strongly
 differentiated between the sites, but differences between species, genets,
 and sexes were not detected. Within S. divinum, however, female
 gametophytes harbored 2-3 times the number of microbial taxa as
 males.  These four Sphagnum species all exhibit similar
 reproductive patterns that result from a mixture of sexual and asexual
 reproduction. The spatial patterns of clonally replicated ramets of genets
 suggest that these species fall between the so-called phalanx patterns
 where genets abut one another but do not extensively mix, because of
 limited ramet fragmentation, and the guerrilla patterns where extensive
 genet fragmentation and dispersal results in greater mixing of different
 genets. Although sex ratios in bryophytes are most often female-biased,
 both male and female biases occur in this complex of closely related
 species. The association of far greater microbial diversity for female
 gametophytes in S. divinum, which has a female-biased sex ratio,
 suggests additional research to determine if levels of microbial diversity
 are consistently correlated with differing patterns of sex ratio biases.
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 or NovaSeq
 6000 with 150bp single-ended reads or HiSeq 2000 with 100bp single-ended
 reads. <strong>"RADseq-like" in silico
 digested genomic data</strong>: 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 number
 of 10 copies (enough to pass downstream depth filters).
description: <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. <strong>File
 demultiplexed_sample_data-radseq1.tar.gz</strong>: Zipped folder
 with100 files of demultiplexed fastq format Illumina reads from RADseq
 samples. <strong>File
 demultiplexed_sample_data-radseq2.tar.gz</strong>: Zipped folder
 with 100 files of demultiplexed fastq format Illumina reads from RADseq
 samples. <strong>File
 demultiplexed_sample_data-radseq3.tar.gz</strong>: Zipped folder
 with 100 files of demultiplexed fastq format Illumina reads from RADseq
 samples. <strong>File
 demultiplexed_sample_data-radseq4.tar.gz</strong>: Zipped folder
 with 100 files of demultiplexed fastq format Illumina reads from RADseq
 samples.