Short stories from Sphagnum of rare species, taxonomy, and speciation.

Conserving species and their genetic variation are a global priority to safeguard evolutionary potential in a rapidly changing world. Species are fundamental units in research and nature management, but taxonomic work is increasingly undermined. Increasing knowledge on the species genetic diversity would aid in prioritizing conservation efforts. Sphagnum is a diverse, well-known bryophyte genus, which makes the genus suited to study speciation and cryptic variation. The species share specific characteristics and can be difficult to separate in the field. By combining molecular data with thorough morphological examination, new species have recently been discovered. Still, there are taxonomic uncertainties, even for species assessed on the IUCN Red List of threatened species. Here, we use molecular data to examine three rare species within the subgenus Acutifolia described based on morphological characters. All species have narrow distributions and limited dispersability. First, we confirm the genetic origin of S. skyense. Second, we show that S. venustum is a haploid species genetically distinct from morphologically similar species. Lastly, S. nitidulum was found to have a distinct haplotype, but cannot be genetically separated from other red Acutifolia species. We also found high genetic variation within red Acutifolia specimens, indicating the need of further morphological examination and possibly taxonomic revision. Until then, our results have shown that genetic data can aid in prioritizing targets of conservation efforts when taxonomy is unresolved. All three taxa should be further searched for by field biologists to increase knowledge about their distribution ranges.

Inclusion of juvenile stages improves diversity assessment and adds to our understanding of mite ecology - A case study from mires in Norway.

Arachnid orders, Mesostigmata, Trombidiformes, and Sarcoptiformes, commonly known as 'mites', are abundant in mires, both as adults and as juveniles. However, due to the challenges of identification, the juvenile forms are often excluded from analyses. This is the first study in mires that included all three mite orders identified to the species level, including juvenile instars. We aimed to compare how diversity and the response to ecological variables differed if only the adults (ad) vs. the total number of specimens (ad+juv) are considered. Samples of 20 Sphagnum species (five subgenera) were collected and mites were extracted using Berlese funnels. Overall, nearly 60,000 mites were analyzed; of these Mesostigmata made up 1.87% of the total, Trombidiformes -0.27%, and Sarcoptiformes -97.86%. The study revealed 154 species (33 Mesostigmata, 24 Trombidiformes, and 97 Sarcoptiformes), the highest diversity of mites ever reported from mires. The inclusion of juveniles increased observed species richness by 6%, with 10 species (one Mesostigmata, six Trombidiformes, and three Sarcoptiformes) represented only by juvenile forms. Seventeen species are new to Norway (four Mesostigmata, one Sarcoptiformes, and 12 Trombidiformes, including five undescribed species of Stigmaeidae and Cunaxidae). Four of these were represented in the samples only by juveniles. Including the juveniles explained a greater amount of the variability of Trombidiformes (explanatory variables account for 23.60% for ad, and 73.74% for ad+juv) and Mesostigmata (29.23% - ad, 52.91% - ad+juv), but had less of an impact for Sarcoptiformes (38.48% - ad, 39.26% - ad+juv). Locality, Sphagnum subgenus and species, wetness, and trophic state significantly affected the mite communities and should be taken into consideration when studying mires. Since juvenile stages contribute significantly to mite diversity in mires, they should also be included in mite studies in other habitats.

Mites (Oribatida and Mesostigmata) and vegetation as complementary bioindicators in peatlands.

Vegetation is widely used in the assessment of the quality of peatlands, while the invertebrate fauna of peatlands is relatively poorly studied. We compared the bioindicator values of vegetation with two arthropod groups widespread in peatlands, saprophagous Oribatida (Acariformes) and predatory Mesostigmata (Parasitiformes) mites. Samples were collected from ecotones at the edges of peatland ponds in Poland, including four in near-natural condition (i.e., peatlands unaffected by human activity) and three in previously disturbed but now recovering peatlands. A set of abiotic parameters was measured at each site: pond area, mean annual temperature, annual precipitation, and water parameters (pH, conductivity, colour, total nitrogen, phosphorus, calcium, and organic carbon). Overall, 63,635 specimens of Oribatida and 448 of Mesostigmata were recovered in the sampling. Species richness of Oribatida (56 species) was higher than that of flora (46) and Mesostigmata (15). Vegetation was significantly associated with annual precipitation in the years 1998-2007 which accounted for 29.1 % of the variation in vegetation communities. Oribatida variability was significantly associated with the content of organic carbon in water accounting for 32.4 % of variation. In contrast, variation in the Mesostigmata was not significantly associated with any of the abiotic parameters. Vegetation at ponds in previously disturbed and now recovering peatlands had higher bush cover than at near-natural ponds and the pond in the cutaway peat had lowest moss cover and the highest number of associate species (i.e., species with wide tolerance not characteristic of the certain community). Mite communities did not differ consistently between near-natural and recovering peatlands. Sphagnum divinum Flatberg et Hassel was recorded from Poland for the first time.

Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta).

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 f4 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.

Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus.

The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.

Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta) in relation to taxonomy and geography.

PREMISE: The Sphagnum recurvum complex comprises a group of closely related peat mosses that are dominant components of many northern wetland ecosystems. Taxonomic hypotheses for the group range from interpreting the whole complex as one polymorphic species to distinguishing 6-10 species. The complex occurs throughout the Northern Hemisphere, and some of the putative species have intercontinental ranges. Our goals were to delimit the complex and assess its phylogenetic structure in relation to morphologically defined species and intercontinental geography. METHODS: RADseq analyses were applied to a sample of 384 collections from Europe, North America, and Asia. The data were subjected to maximum likelihood phylogenetic analyses and analyses of genetic structure using the software STRUCTURE and multivariate ordination approaches. RESULTS: The S. recurvum complex includes S. angustifolium, S. fallax, S. flexuosum, S. pacificum, and S. recurvum as clades with little evidence of admixture. We also resolved an unnamed clade that is referred to here as S. "pseudopacificum." We confirm that S. balticum and S. obtusum are nested within the complex. Species with bluntly acute to obtuse stem leaf apices are sister to those with acute to apiculate leaves. Most of the species exhibit some differentiation between intraspecific population systems disjunct on different continents. CONCLUSIONS: We recognize seven species in the amended S. recurvum complex, including S. balticum and S. obtusum, in addition to the informal clade S. "pseudopacificum." Although we detected some geographically correlated phylogenetic structure within widespread morphospecies, our RADseq data support the interpretation that these species have intercontinental geographic ranges.

Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum.

PREMISE OF THE STUDY: Populations with phenotypic polymorphism in discrete characters may be good models for investigating genome evolution and speciation. Sphagnum magellanicum Brid. is found throughout the northern hemisphere, and despite considerable variation in morphological characters, it is considered one of the least taxonomically controversial peatmoss species. We have observed two main morphs of the species associated with different microhabitats. Here we investigated the genomic and environmental basis of this intraspecific morphological variation. METHODS: We conducted transplant and common garden experiments to test whether the two morphs are genetically differentiated. We then used RAD-sequencing to quantify the genomic divergence between the morphs and approximate Bayesian computation (ABC) to infer the most likely demographic scenario explaining the genome-wide differentiation of the two morphs. KEY RESULTS: We found that genomic differentiation between the two morphs is unexpectedly high and that several of the differentiated morphological characters have a genetic basis. Using simulation approaches, we found support for a scenario of ancient divergence followed by recent secondary contact. CONCLUSIONS: We show that the two morphs represent the two main genetic clusters previously found worldwide. Our results demonstrate that relatively minor morphological differentiation in a presumed phenotypically plastic peatmoss may be associated with massive divergence across the genome.

Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss).

BACKGROUND AND AIMS: Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided. METHODS: We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium KEY RESULTS: Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium CONCLUSIONS: Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.

Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.