Neckera, Forsstroemia and Alleniella (Neckeraceae, Bryophyta) redefined based on phylogenetic analyses

Phylogenetic relationships of species within the pleurocarpous moss genus Neckera s.l. (Neckeraceae) are reconstructed based on three genomic regions: the plastid rps4-trnT-trnL-trnF cluster and the rpl16 group II intron, as well as the internal transcribed spacer region of the nuclear ribosomal DNA (ITS1-5.8S-ITS2). The phylogenetic reconstruction suggests numerous taxonomic changes within the Neckeraceae. Two unispecific Asian genera are described as new: Taiwanobryopsis to accommodate Neckera warburgii, and Indoneckera to accommodate Neckera himalayana. Seven of the other "Neckera" species, all distributed in Asia, are transferred to Forsstroemia, and a further four Asian species to Taiwanobryum. Six Southern Hemisphere or tropical species (one from New Zealand, one from Africa, four from South America) are transferred to Alleniella. After these adjustments, Neckera becomes a northern hemisphere, mainly temperate, genus of c. 10 species that are absent from the tropics. It is in this context morphologically characterized by lack of paraphyllia (except N. californica) and an absent or weak costa. Alleniella has two species-the first diverging lineages-in the northern hemisphere, but the rest of the currently 15 species are distributed in the southern hemisphere and most of the species occur in mountain habitats in the tropics; it is however absent from tropical Asia and very scarce in Asia in general. Twelve of the 15 species have paraphyllia, which is the clearest morphological distinction from Neckera. Forsstroemia with 19 species, heavily concentrated in Asia, is the largest genus in the Neckeraceae. Clearly longer and more distinct costa distinguishes the genus from Neckera and Alleniella. Taiwanobryum is a morphologically heterogeneous Asian genus of nine species. Neckera decurrens Broth. is synonymized with Forsstroemia fauriei and Neckera valentiniana Besch. with Alleniella ehrenbergii.Peer reviewe

Cebadores universales para la amplificación de la región del plasto trnK/matK en plantas terrestres

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A century later – Pinnatella gollanii is still alive!

Pinnatella gollanii Broth., previously known only from north Indian collections dating back to 1903, was rediscovered in Nepal in 2001.Peer reviewe

Historical assembly of Zygophyllaceae in the Atacama Desert

The Atacama Desert harbors a unique arid-adapted flora with a high degree of endemism, the origin of which is poorly understood. In the Atacama Desert, Zygophyllaceae is represented by five endemic species: one member of Zygophylloideae: Fagonia chilensis; and four members of Larreoideae: Bulnesia chilensis and Porlieria chilensis, the only representatives in the Atacama Desert of genera with disjunct distributions between Argentina, Peru and Chile; and monotypic endemic genera Metharme lanata and Pintoa chilensis. Zygophyllaceae are thus a particularly suitable group for studying the historical assembly of the Atacama Desert flora as each of these species may represent independent biogeographical events. We made use of published as well as original plastid DNA sequences (rbcL, trnL-trnF & trnS-trnG) to reevaluate the phylogenetic relationships of the Atacama Zygophyllaceae. Bayesian divergence time estimates as implemented in BEAST2 and ancestral area reconstruction with the Dispersal Extinction Cladogenesis approach using BioGeoBEARS were applied to infer ancestral ranges. We compiled the most complete data set of Larreoideae to date with 25 of 28 species. Bulnesia rivas-martinezii from Bolivia forms a clade with Pintoa chilensis from the Atacama Desert, rendering the genus Bulnesia paraphyletic. Most representatives of Zygophyllaceae colonized the Atacama Desert during the Miocene, and only Fagonia dispersed more recently. The colonization history of the Atacama Desert in South America is reflected by three individual distribution patterns or floristic elements. The presence of Bulnesia, Pintoa, and Metharme is best explained by Andean vicariance, while the southern Atacama Desert representative, Porlieria chilensis, has a continuous distribution into central Chile from where it probably dispersed further north. The only South American Fagonia species (F. chilensis) likely colonized the Chilean-Peruvian Coastal Desert via long distance dispersal from North America

Phylogenetic analyses reveal high levels of polyphyly among pleurocarpous lineages as well as novel clades

Phylogenetic analyses of the Hypnales usually show the same picture of poorly resolved trees with a large number of polyphyletic taxa and low support for the few reconstructed clades. One odd clade, however, consisting of three genera that are currently treated either within the Leskeaceae (Miyabea) or Neckeraceae (Homaliadelphus and Bissetia), was retrieved in a previously published phylogeny based on chloroplast rbcL. In order to elucidate the reliability of the observed Homaliadelphus - Miyabea - Bissetia - clade (HMB-clade) and to reveal its phylogenetic relationships a molecular study based on a representative set of hypnalean taxa was performed. Sequence data from all three genomes, namely the ITS1 and 2 (nuclear), the trnS-rps4-trnT-trnL-trnF cluster (plastid), the nad5 intron (mitochondrial), were analyzed. Although the phylogenetic reconstruction of the combined data set was not fully resolved regarding the backbone it clearly indicated the polyphyletic nature of various hypnalean families, such as the Leskeaceae, Hypnaceae, Hylocomiaceae, Neckeraceae, Leptodontaceae and Anomodontaceae with respect to the included taxa. In addition the results favor the inclusion of the Leptodontaceae and Thamnobryaceae in the Neckeraceae. The maximally supported HMB-clade consisting of the three genera Homaliadelphus (2-3 species), Miyabea (3 species) and Bissetia (1 species) is resolved sister to a so far unnamed clade comprising Taxiphyllum aomoriense, Glossadelphus ogatae and Leptopterigynandrum. The well-resolved and supported HMB-clade, here formally described as the Miyabeaceae, fam. nov. is additionally supported by morphological characters such as strongly incrassate, porose leaf cells, a relatively weak and diffuse costa and the presence of dwarf males. The latter are absent in the Neckeraceae and the Leskeaceae. It is essentially an East Asian family, with one species occurring in North America.Phylogenetic analyses of the Hypnales usually show the same picture of poorly resolved trees with a large number of polyphyletic taxa and low support for the few reconstructed clades. One odd clade, however, consisting of three genera that are currently treated either within the Leskeaceae (Miyabea) or Neckeraceae (Homaliadelphus and Bissetia), was retrieved in a previously published phylogeny based on chloroplast rbcL. In order to elucidate the reliability of the observed Homaliadelphus - Miyabea - Bissetia - clade (HMB-clade) and to reveal its phylogenetic relationships a molecular study based on a representative set of hypnalean taxa was performed. Sequence data from all three genomes, namely the ITS1 and 2 (nuclear), the trnS-rps4-trnT-trnL-trnF cluster (plastid), the nad5 intron (mitochondrial), were analyzed. Although the phylogenetic reconstruction of the combined data set was not fully resolved regarding the backbone it clearly indicated the polyphyletic nature of various hypnalean families, such as the Leskeaceae, Hypnaceae, Hylocomiaceae, Neckeraceae, Leptodontaceae and Anomodontaceae with respect to the included taxa. In addition the results favor the inclusion of the Leptodontaceae and Thamnobryaceae in the Neckeraceae. The maximally supported HMB-clade consisting of the three genera Homaliadelphus (2-3 species), Miyabea (3 species) and Bissetia (1 species) is resolved sister to a so far unnamed clade comprising Taxiphyllum aomoriense, Glossadelphus ogatae and Leptopterigynandrum. The well-resolved and supported HMB-clade, here formally described as the Miyabeaceae, fam. nov. is additionally supported by morphological characters such as strongly incrassate, porose leaf cells, a relatively weak and diffuse costa and the presence of dwarf males. The latter are absent in the Neckeraceae and the Leskeaceae. It is essentially an East Asian family, with one species occurring in North America.Phylogenetic analyses of the Hypnales usually show the same picture of poorly resolved trees with a large number of polyphyletic taxa and low support for the few reconstructed clades. One odd clade, however, consisting of three genera that are currently treated either within the Leskeaceae (Miyabea) or Neckeraceae (Homaliadelphus and Bissetia), was retrieved in a previously published phylogeny based on chloroplast rbcL. In order to elucidate the reliability of the observed Homaliadelphus - Miyabea - Bissetia - clade (HMB-clade) and to reveal its phylogenetic relationships a molecular study based on a representative set of hypnalean taxa was performed. Sequence data from all three genomes, namely the ITS1 and 2 (nuclear), the trnS-rps4-trnT-trnL-trnF cluster (plastid), the nad5 intron (mitochondrial), were analyzed. Although the phylogenetic reconstruction of the combined data set was not fully resolved regarding the backbone it clearly indicated the polyphyletic nature of various hypnalean families, such as the Leskeaceae, Hypnaceae, Hylocomiaceae, Neckeraceae, Leptodontaceae and Anomodontaceae with respect to the included taxa. In addition the results favor the inclusion of the Leptodontaceae and Thamnobryaceae in the Neckeraceae. The maximally supported HMB-clade consisting of the three genera Homaliadelphus (2-3 species), Miyabea (3 species) and Bissetia (1 species) is resolved sister to a so far unnamed clade comprising Taxiphyllum aomoriense, Glossadelphus ogatae and Leptopterigynandrum. The well-resolved and supported HMB-clade, here formally described as the Miyabeaceae, fam. nov. is additionally supported by morphological characters such as strongly incrassate, porose leaf cells, a relatively weak and diffuse costa and the presence of dwarf males. The latter are absent in the Neckeraceae and the Leskeaceae. It is essentially an East Asian family, with one species occurring in North America.Peer reviewe

Phylogeny-Based Comparative Methods Question the Adaptive Nature of Sporophytic Specializations in Mosses

Adaptive evolution has often been proposed to explain correlations between habitats and certain phenotypes. In mosses, a high frequency of species with specialized sporophytic traits in exposed or epiphytic habitats was, already 100 years ago, suggested as due to adaptation. We tested this hypothesis by contrasting phylogenetic and morphological data from two moss families, Neckeraceae and Lembophyllaceae, both of which show parallel shifts to a specialized morphology and to exposed epiphytic or epilithic habitats. Phylogeny-based tests for correlated evolution revealed that evolution of four sporophytic traits is correlated with a habitat shift. For three of them, evolutionary rates of dual character-state changes suggest that habitat shifts appear prior to changes in morphology. This suggests that they could have evolved as adaptations to new habitats. Regarding the fourth correlated trait the specialized morphology had already evolved before the habitat shift. In addition, several other specialized “epiphytic” traits show no correlation with a habitat shift. Besides adaptive diversification, other processes thus also affect the match between phenotype and environment. Several potential factors such as complex genetic and developmental pathways yielding the same phenotypes, differences in strength of selection, or constraints in phenotypic evolution may lead to an inability of phylogeny-based comparative methods to detect potential adaptations.Peer reviewe

BarKeeper—a versatile web framework to assemble, analyse and manage DNA barcoding data and metadata

1. DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high‐quality sequences to maximize identification success. 2. BarKeeper provides a flexible tool for barcoding initiatives and in the context of phylogenetic studies to foster shared work on large datasets of raw sequence and associated metadata. It is free, open‐source and available as a set of Docker containers for easy setup. After setting it up once, all project members can use it independently of their operating system or location. 3. BarKeeper offers features to collect and manage data and metadata about specimens, taxa and DNA sequences from Sanger sequencing and high‐throughput sequencing (HTS) technologies. It provides excellent flexibility by not being restricted to specific markers or taxon groups. Users can view and edit records and associated metadata while the app assists them by trimming and assembling reads. It automatically checks the quality of generated barcodes with a taxonomy‐based tool and offers a wide range of options for data analysis. Extensive search features allow querying the database for specific groups of records and saving the search results in the user's profile or downloading them in various file formats. 4. BarKeeper combines multiple tools to aid barcoding projects in every step, from a reference taxa list to finished barcode sequences, thereby minimizing the number of laborious, potentially error‐prone manual steps and enabling efficient collaborative workflows

Phylogeny of Neckeropsis and Himantocladium (Neckeraceae, Bryophytina)

Two closely related tropical genera from the pleurocarpous moss family Neckeraceae are revised: the second largest genus in the family, Neckeropsis, currently with 29 species, and Himantocladium, comprising six species. Twenty-one species of Neckeropsis and five of Himantocladium were included in this study, which is based on phylogenetic analyses using sequence level data from the plastid (rps4)-trnT-trnL-trnF cluster and rpl16 as well as nuclear ITS1 & 2. Neckeropsis appeared as polyphyletic. Neckeropsis s. str. comprises 12 species and a further four species, not included in the analysis, are tentatively retained in the genus based on morphology. Four new genera are segregated from Neckeropsis: Pengchengwua (with one sp.), Planicladium (two spp.), Pseudoparaphysanthus (five spp.), and Neckeromnion (five spp.). Neckeropsis gracilis is synonymized with Neckeromnion urocladum and reported for the first time from Laos. Four molecular analyzed species are resolved in the Himantocladium s. str. clade, with a fifth species being added solely on morphological basis. Himantocladium formosicum is transferred to Neckeropsis. Leaf-like paraphyses (ramenta), unique in Neckeropsis s. str., have evolved two times. In addition, the rare Noguchiodendron sphaerocarpum from the Himalayan region, the single species in its genus, was included in a phylogenetic analysis for the first time and it was found to be closely related to the Asian genus Taiwanobryum.Peer reviewe

Liverworts show a globally consistent mid‐elevation richness peak

The study of elevational gradients allows to draw conclusions on the factors and mechanisms determining patterns in species richness distribution. Several earlier studies investigated liverwort diversity on single or few elevational transects. However, a comprehensive survey of the elevational distribution patterns of liverwort richness and their underlying factors is lacking so far. This study's purpose was to fill this gap by compiling an extensive data set of liverwort elevational patterns encompassing a broad diversity of mountains and mountain ranges around the world. Using polynomial regression analyses, we found a prevalence of hump‐shaped richness patterns (19 of 25 gradients), where liverwort species richness peaked at mid‐elevation and decreased towards both ends of the gradient. Against our expectation and unlike in other plant groups, in liverworts, this pattern also applies to elevational gradients at mid‐latitudes in temperate climates. Indeed, relative elevation, calculated as the percentage of the elevational range potentially inhabited by liverworts, was the most powerful predictor for the distribution of liverwort species richness. We conclude from these results that the admixture of low‐ and high‐elevation liverwort floras, in combination with steep ecological gradients, leads to a mid‐elevation floristic turnover shaping elevational patterns of liverwort diversity. Our analyses further detected significant effects of climatic variables (temperature of the warmest month, potential evapotranspiration, and precipitation of the warmest month) in explaining elevational liverwort richness patterns. This indicates that montane liverwort diversity is restricted by high temperatures and subsequent low water availability especially towards lower elevations, which presumably will lead to serious effects by temperature shifts associated with global warming