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Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics.Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples.We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f 4 ratios. One ecologically important functional trait, tissue decomposability, which underlies peat (carbon) accumulation, does not differ between segregates in the S. magellanicum complex, although previous research showed that many closely 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.

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Population size changes and gene flow are processes that can have significant impacts on evolution. The aim of this study was to investigate the relationship of geography to patterns of gene flow and population size changes in a pair of closely related Sphagnum (peatmoss) species: S. recurvum and S. flexuosum . Both species occur in eastern North America, and S. flexuosum also occurs in Europe. Genetic data from restriction‐site‐associated DNA sequencing (RAD‐seq) were used in this study. Analyses of gene flow were accomplished using coalescent simulations of site frequency spectra (SFSs). Signatures of gene flow were confirmed by f 4 statistics. For S. flexuosum , genetic diversity of plants in glaciated areas appeared to be lower than that in unglaciated areas, suggesting that glaciation can have an impact on effective population sizes. There is asymmetric gene flow from eastern North America to Europe, suggesting that Europe might have been colonized by plants from eastern North America after the last glacial maximum. The rate of gene flow between S. flexuosum and S. recurvum is lower than that between geographically disjunct S. flexuosum populations. The rate of gene flow between species is higher among sympatric plants of the two species than between currently allopatric S. flexuosum populations. There was also gene flow from S. recurvum to the ancestor S. flexuosum on both continents which occurred through secondary contact. These results illustrate a complex history of interspecific gene flow between S. flexuosum and S. recurvum , which occurred in at least two phases: between ancestral populations after secondary contact and between currently sympatric plants.

New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species, Sphagnum magellanicum, is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. We find using sliding-window population genetic analyses that differentiation is concentrated within “islands” of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity, and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism, and hormone-mediated signaling. Demographic modeling demonstrates that these two species diverged no more than 225,000 generations ago with secondary contact occurring where their ranges overlap. We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth’s climate rapidly changes.