Data from: Clonality, local population structure, and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex
Data files
Jun 23, 2023 version files 86.82 GB
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demultiplexed_sample_data-insilico.tar.gz
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demultiplexed_sample_data-radseq1.tar.gz
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demultiplexed_sample_data-radseq2.tar.gz
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demultiplexed_sample_data-radseq3.tar.gz
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demultiplexed_sample_data-radseq4.tar.gz
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md5sum.txt
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README.md
Abstract
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.
Methods
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 number of 10 copies (enough to pass downstream depth filters).
Usage notes
File demultiplexed_sample_data-insilico.tar.gz: Zipped folder with 43 files of fastq format "RADseq-like" reads from in silico digested genome resequencing samples.
File demultiplexed_sample_data-radseq1.tar.gz: Zipped folder with100 files of demultiplexed fastq format Illumina reads from RADseq samples.
File demultiplexed_sample_data-radseq2.tar.gz: Zipped folder with 100 files of demultiplexed fastq format Illumina reads from RADseq samples.
File demultiplexed_sample_data-radseq3.tar.gz: Zipped folder with 100 files of demultiplexed fastq format Illumina reads from RADseq samples.
File demultiplexed_sample_data-radseq4.tar.gz: Zipped folder with 100 files of demultiplexed fastq format Illumina reads from RADseq samples.