We present a complete generic‐level phylogeny of the complex thalloid liverworts, a lineage that includes the model system Marchantia polymorpha. The complex thalloids are remarkable for their slow ...rate of molecular evolution and for being the only extant plant lineage to differentiate gas exchange tissues in the gametophyte generation. We estimated the divergence times and analyzed the evolutionary trends of morphological traits, including air chambers, rhizoids and specialized reproductive structures. A multilocus dataset was analyzed using maximum likelihood and Bayesian approaches. Relative rates were estimated using local clocks. Our phylogeny cements the early branching in complex thalloids. Marchantia is supported in one of the earliest divergent lineages. The rate of evolution in organellar loci is slower than for other liverwort lineages, except for two annual lineages. Most genera diverged in the Cretaceous. Marchantia polymorpha diversified in the Late Miocene, giving a minimum age estimate for the evolution of its sex chromosomes. The complex thalloid ancestor, excluding Blasiales, is reconstructed as a plant with a carpocephalum, with filament‐less air chambers opening via compound pores, and without pegged rhizoids. Our comprehensive study of the group provides a temporal framework for the analysis of the evolution of critical traits essential for plants during land colonization.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Because hornworts occupy a pivotal position in early land colonization as sister to other bryophytes, sister to tracheophytes, or sister to all other land plants, a renewed interest has arisen in ...their phylogenetic diversity, morphology, and genomes. To date, only five organellar genome sequences are available for hornworts. We sequenced the plastome (155,956 bp) and mitogenome (212,153 bp) of the hornwort Leiosporoceros dussii, the sister taxon to all hornworts. The Leiosporoceros organellar genomes show conserved gene structure and order with respect to the other hornworts and other bryophytes. Additionally, using RNA-seq data we quantified the frequency of RNA-editing events (the canonical C-to-U and the reverse editing U-to-C) in both organellar genomes. In total, 109 sites were found in the plastome and 108 in the mitogenome, respectively. The proportion of edited sites corresponds to 0.06% of the plastome and 0.05% of the mitogenome (in reference to the total genome size), in contrast to 0.58% of edited sites in the plastome of Anthoceros angustus (161,162 bp). All edited sites in the plastome and 88 of 108 sites in the mitogenome are C-to-U conversions. Twenty reverse edited sites (U-to-C conversions) were found in the mitogenome (17.8%) and none in the plastome. The low frequency of RNA editing in Leiosporoceros, which is nearly 88% less than in the plastome of Anthoceros and the mitogenome of Nothoceros, indicates that the frequency of RNA editing has fluctuated during hornwort diversification. Hornworts are a pivotal land plant group to unravel the genomic implications of RNA editing and its maintenance despite the evident evolutionary disadvantages.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cyanobacteria have played pivotal roles in Earth’s geological history, especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution ...has been limited by their extremely lopsided tree of life—the vast majority of extant diversity belongs to Phycobacteria (or “crown Cyanobacteria”), while its sister lineage, Gloeobacteria, is depauperate and contains only two closely related species of Gloeobacter and a metagenome-assembled genome. Here, we describe a new cultured member of Gloeobacteria, Anthocerotibacter panamensis, isolated from a tropical hornwort. Anthocerotibacter diverged from Gloeobacter over 1.4 Ga ago and has low 16S rDNA identities with environmental samples. Our ultrastructural, physiological, and genomic analyses revealed that this species possesses a unique combination of traits that are exclusively shared with either Gloeobacteria or Phycobacteria. For example, similar to Gloeobacter, it lacks thylakoids and circadian clock genes, but the carotenoid biosynthesis pathway is typical of Phycobacteria. Furthermore, Anthocerotibacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerotibacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency. Given its key phylogenetic position, distinct trait combination, and availability as a culture, Anthocerotibacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.
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•A new thylakoid-less cyanobacterium cultured from a tropical hornwort•This isolate is sister to a clade of environmental samples from the polar regions•It diverged >1.4 Ga ago from the closest cultured taxa, Gloeobacter spp.•Unique gene repertoires of phycobilisome and photosystems were uncovered
Very few cultured species exist in Gloeobacteria, an enigmatic lineage that is sister to the crown Cyanobacteria. Rahmatpour et al. discover a new and deeply diverged member of Gloeobacteria. This new species exhibits a suite of unique morphological, physiological, and genomic features, thus shedding new light on the evolution of Cyanobacteria.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Lichens cover nearly 7% of the earth’s surface, and in eastern Canada, lichen woodlands occupy over 300 000 km
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. Reindeer lichens (genus Cladonia) are the main component of lichen woodlands and ...they play a crucial role in boreal forest ecology. We study, for the first time, the bacterial community of four species of reindeer lichens from eastern North America’s boreal forests. Using the 16S rRNA gene, we characterize the bacterial community of 189 lichen samples. We aim to analyse the effect of geography and host identity in the bacterial community composition and structure, verify the presence of a common core bacteria, and identify the most abundant core taxa. Our results suggest that host-lichen identity does not determine bacterial community composition and structure in reindeer lichens, but we confirm the influence of geography in shaping the diversity and abundance of bacteria associated with Cladonia stellaris. We also reveal that reindeer lichens share a reduced common core bacteria composed exclusively by Alphaproteobacteria. Northern lichen woodlands exhibit a significantly higher diversity and abundance of bacteria associated with C. stellaris than southern lichen woodlands do. The presence of the species Methylorosula polaris in the core bacteria is evident and may have a particular importance for reindeer lichens.
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BF, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Premise
Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and ...mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear.
Methods
Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.
Results
The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene‐tree topology.
Conclusions
We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Aim: We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis ...that the species arose in Macaronesia (neo-endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo-endemism). Location: Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods: DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)-based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results: The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo-endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south-western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions: The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long-distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo-endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Analyze the measurement invariance and the factor structure of the Patient Health Questionnaire-9 (PHQ-9) in the Peruvian population.
Secondary data analysis performed using cross-sectional data from ...the Health Questionnaire of the Demographic and Health Survey in Peru. Variables of interest were the PHQ-9 and demographic characteristics (sex, age group, level of education, socioeconomic status, marital status, and area of residence). Factor structure was evaluated by standard confirmatory factor analysis (CFA), and measurement invariance by multi-group CFA, using standard goodness-of-fit indices criteria for interpreting results from both CFAs. Analysis of the internal consistency (α and ω) was also pursued.
Data from 30,449 study participants were analyzed, 56.7% were women, average age was 40.5 years (standard deviation (SD) = 16.3), 65.9% lived in urban areas, 74.6% were married, and had 9 years of education on average (SD = 4.6). From standard CFA, a one-dimensional model presented the best fit (CFI = 0.936; RMSEA = 0.089; SRMR = 0.039). From multi-group CFA, all progressively restricted models had ΔCFI<0.01 across almost all groups by demographic characteristics. PHQ-9 reliability was optimal (α = ω = 0.87).
The evidence presents support for the one-dimensional model and measurement invariance of the PHQ-9 measure, allowing for reliable comparisons between sex, age groups, education level, socioeconomic status, marital status, and residence area, and recommends its use within the Peruvian population.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
PREMISE
Lichens are one of the main structural components of plant communities in the North American boreal biome. They play a pivotal role in lichen woodlands, a large ecosystem situated north of ...the closed‐crown forest zone, and south of the forest–tundra zone. In Eastern Canada (Quebec), there is a remnant LW found 500 km south of its usual distribution range, in the Parc National des Grands‐Jardins, originated mainly because of wildfires. We inferred the origin of the lichen Cladonia stellaris from this LW and assessed its genetic diversity in a postfire succession.
METHODS
We genotyped 122 individuals collected across a latitudinal gradient in Quebec. Using the software Stacks, we compared four different approaches of locus selection and single‐nucleotide polymorphism calling. We identified the best fitting approach to investigate population structure and estimate genetic diversity of C. stellaris.
RESULTS
Populations in southern Quebec are not genetically different from those of northern LWs. The species consists of at least four phylogenetic lineages with elevated levels of genetic diversity and low co‐ancestry. In Parc National des Grands‐Jardins, we reported high values of genetic diversity not related with time since fire disturbance and low genetic differentiation among populations with different fire histories.
CONCLUSIONS
This first population genomic study of C. stellaris is an important step forward to understand the origin and biogeographic patterns of lichen woodlands in North America. Our findings also contribute to the understanding of the effect of postfire succession on the genetic structure of the species.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Ribulose-1,5-Biphosphate-carboxylase-oxygenase (RuBisCO) has a crucial role in carbon fixation but a slow catalytic rate, a problem overcome in some plant lineages by physiological and anatomical ...traits that elevate carbon concentrations around the enzyme. Such carbon-concentrating mechanisms are hypothesized to have evolved during periods of low atmospheric CO ₂. Hornworts, the sister to vascular plants, have a carbon-concentrating mechanism that relies on pyrenoids, proteinaceous bodies mostly consisting of RuBisCO. We generated a phylogeny based on mitochondrial and plastid sequences for 36% of the approximately 200 hornwort species to infer the history of gains and losses of pyrenoids in this clade; we also used fossils and multiple dating approaches to generate a chronogram for the hornworts. The results imply five to six origins and an equal number of subsequent losses of pyrenoids in hornworts, with the oldest pyrenoid gained ca . 100 Mya, and most others at <35 Mya. The nonsynchronous appearance of pyrenoid-containing clades, the successful diversification of pyrenoid-lacking clades during periods with low CO ₂, and the maintenance of pyrenoids during episodes of high CO ₂ all argue against the previously proposed relationship between pyrenoid origin and low CO ₂. The selective advantages, and costs, of hornwort pyrenoids thus must relate to additional factors besides atmospheric CO ₂.
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