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![Revised species identifications in the Racomitrium canescens species complex based on molecular data. Changes in species identification of 14 specimens analyzed in the present study are indicated by arrows. Arrow thickness is equivalent to the number of specimens transferred from one species to another (one, two, or four specimens, respectively). Grey or black arrows indicate changes within or between subsections Canescens and Ericoides [15], respectively. doi:10.1371/journal.pone.0053134.g003](profile/Kristian-Hassel/publication/235364282/figure/fig5/AS:669635196223492@1536664880404/Revised-species-identifications-in-the-Racomitrium-canescens-species-complex-based-on.png)
Revised species identifications in the Racomitrium canescens species complex based on molecular data. Changes in species identification of 14 specimens analyzed in the present study are indicated by arrows. Arrow thickness is equivalent to the number of specimens transferred from one species to another (one, two, or four specimens, respectively). Grey or black arrows indicate changes within or between subsections Canescens and Ericoides [15], respectively. doi:10.1371/journal.pone.0053134.g003
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In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from...
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... (e.g. collections provisionally named R. canescens [sensu lato] to indicate that they belong to the complex), but might also be an inherent problem of the diagnostic characters. The majority of the 14 misidentified specimens belonged to species of subsection Ericoides sensu Frisvoll [17], not to R. canescens s.str. or subsp. latifolium (Fig. 3). Morphological re-investigation revealed that some of the collections named R. canescens, but actually belonging to R. ericoides or R. elongatum, were intermediate in terms of the diagnostic characters separating these three species. They showed rather broad and obtusely keeled leaves, typical for R. canescens, but a single, non-forked ...
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DNA sequences have been widely used for taxonomy, inferring phylogenetic relationships and identifying species boundaries. Several specific methods to define species delimitations based on molecular phylogenies have appeared recently, with the generalized mixed Yule coalescent (GMYC) method being most popular. However, only few studies on land plan...
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... Among other outcomes, the use of integrative taxonomy has helped to unravel that some taxa traditionally treated as single species are complexes of species. Newly unveiled species often exhibit narrower distribution ranges than those previously attributed under the initial species 2 • Matanov et al. circumscription (Medina et al. 2012, Stech et al. 2013, Lee et al. 2022) directly affecting the conservation and preservation of biodiversity. ...
The bryophyte genus Ulota has its main diversification area in Patagonia, with 18 currently accepted species, all of which are endemic to the area. Despite this richness, ongoing studies indicate the existence of hitherto unknown species in this territory. However, the strong resemblance between species often complicates the discrimination of new taxa, making the use of integrative taxonomy approaches compulsory. During surveys conducted in past decades, a morphotype of a Ulota, closely resembling Ulota macrodontia, was discovered coexisting with this species. Ulota macrodontia is characterized by unique peristomial features within the genus, and the variant morphotype shares these characteristics while displaying some distinct gametophytic and sporophytic features. Biometric analyses demonstrate that the differences are stable, and without intermediate states. The results obtained from the analyses of one nuclear and four plastid loci reveal a close relationship between both morphotypes, with the samples of U. macrodontia forming a well-supported monophyletic group. We propose to treat the new morphotype at species level (Ulota brachypoda sp. nov.), discussing why this is the most appropriate taxonomic rank, and we provide a detailed and illustrated description. Additionally, a distribution map of the two endemics is included.
... One is the morphological differences serve as the basis for taxonomic hypotheses that are validated using genetic data (e.g., Gugerli et al., 2007;Welton et al., 2013). The other is interpreted as morphologic variation in the context of identification from genetic data as a robust methodology to support the results of species identification (e.g., Liu et al., 2018;Stech et al., 2013). In our study, we used the latter approach for species identification of the two oaks using genetic analysis as a priori. ...
Plant phenotypic characteristics, especially leaf morphology of leaves, are an important indicator for species identification. However, leaf shape can be extraordinarily complex in some species, such as oaks. The great variation in leaf morphology and difficulty of species identification in oaks have attracted the attention of scientists since Charles Darwin. Recent advances in discrimination technology have provided opportunities to understand leaf morphology variation in oaks. Here, we aimed to compare the accuracy and efficiency of species identification in two closely related deciduous oaks by geometric morphometric method (GMM) and deep learning using preliminary identification of simple sequence repeats (nSSRs) as a prior. A total of 538 Asian deciduous oak trees, 16 Q. aliena and 23 Q. dentata populations, were firstly assigned by nSSRs Bayesian clustering analysis to one of the two species or admixture and this grouping served as a priori identification of these trees. Then we analyzed the shapes of 2328 leaves from the 538 trees in terms of 13 characters (landmarks) by GMM. Finally, we trained and classified 2221 leaf‐scanned images with Xception architecture using deep learning. The two species can be identified by GMM and deep learning using genetic analysis as a priori. Deep learning is the most cost‐efficient method in terms of time‐consuming, while GMM can confirm the admixture individuals' leaf shape. These various methods provide high classification accuracy, highlight the application in plant classification research, and are ready to be applied to other morphology analysis.
... These acrocarpic mosses are particularly abundant in the forest-tundra ecotone compared to feather mosses and Sphagnum spp., forming large mats (Gordon et al. 2001;Cutler 2011) and, thus, may represent an essential entry of N 2 through their associated diazotrophic bacteria. For example, the genus Racomitrium is widely distributed in the northern hemisphere from North America to arctic and sub-artic Eurasia (Vitt and Marsh 1988;Larraín et al. 2013;Stech et al. 2013;Hedenäs 2020;Escolástico-Ortiz et al. 2023), covering up to 20 million km 2 in Europe (Hodgetts 2019). Reports on N 2 -fixation rates indicate that Racomitrium spp. ...
Bryophytes maintain symbiosis with bacteria influencing the local nutrient budget. Moss bacterial communities are composed of a core microbiome and bacteria recruited from environmental sources. Notably, symbiotic N2-fixing bacteria contribute to the N budget in northern ecosystems through biological nitrogen fixation. This process may be affected by the abundance of diazotrophs and moss nutrient content. We used the abundant moss Racomitrium lanuginosum in a forest tundra and shrub tundra in Northern Quebec, Canada, to investigate the bacterial and diazotrophic communities associated with habitat type using amplicon sequencing of the bacterial 16S rRNA and nifH genes and test whether the moss core microbiome has recruitment from the soil bacteria community. The nifH amplicons and element analysis were used to test the effect of diazotrophic abundance and moss nutrient content on N2-fixation activity estimated by acetylene reduction assays. Moss microbial communities between tundra types hosted similar bacterial diversity but differentially abundant groups and characteristic microbial interaction patterns. The core microbiome of R. lanuginosum is composed of bacteria strongly associated with northern mosses with no significant recruitment from the soil. The relative abundances of dominant diazotrophs are significantly correlated with acetylene reduction rates. In contrast, the moss nutrient content did not significantly drive N2-fixation. The proteobacterial genera Azorhizobium and Rhodomicrobium represent newly reported bacteria associated with N2-fixation rates in the tundra. We identified critical bacterial groups related to moss-bacterial symbiosis and N2-fixation in the forest-tundra transition zone, a changing environment susceptible to climate warming.
... In addition, it should be short enough to be recovered from degraded tissue such as highly processed materials or forensic samples (Chase et al., 2007). As a principle, this method utilizes the genetic variation among species to distinguish organisms (Hebert et al., 2003), in which a sequence of an unidentified specimen is compared to a sequence database of identified sequences (Stech et al., 2013). ...
... DNA barcode reference databases can be useful for much more than just instances where morphological identification is difficult (or not available), but in fact, be applied as supplemental TA B L E 3 Test for monophyly results at species level for the Burseraceae samples used in this study based on the matK Bayesian inference. tool in addition to the conventional taxonomy in identification and classification of cryptic species (Hartvig et al., 2015;Stech et al., 2013). Additionally, it may be incorporated for post hoc 'molecular' identifications, where specimens' identification is confirmed afterward by taxonomists with access to the voucher herbarium specimens and molecular species assignments, as conducted in this study. ...
The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short-lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.
... Hoary fringe-moss (Racomitrium canescens) is a globally distributed, desiccationtolerant moss species belonging to the family Grimmiaceae [3,28]. R. canescens is resistant to desiccation, possessing a good water storage capacity (i.e., 8-10 times its dry weight) [29,30]; however, the mechanism underlying its desiccation tolerance and rapid rehydration capacity has not been explored in detail. ...
The moss Racomitrium canescens (R. canescens) has strong desiccation tolerance. It can remain desiccated for years and yet recover within minutes of rehydration. Understanding the responses and mechanisms underlying this rapid rehydration capacity in bryophytes could identify candidate genes that improve crop drought tolerance. We explored these responses using physiology, proteomics, and transcriptomics. Label-free quantitative proteomics comparing desiccated plants and samples rehydrated for 1 min or 6 h suggesting that damage to chromatin and the cytoskeleton had occurred during desiccation, and pointing to the large-scale degradation of proteins, the production of mannose and xylose, and the degradation of trehalose immediately after rehydration. The assembly and quantification of transcriptomes from R. canescens across different stages of rehydration established that desiccation was physiologically stressful for the plants; however, the plants recovered rapidly once rehydrated. According to the transcriptomics data, vacuoles appear to play a crucial role in the early stages of R. canescens recovery. Mitochondria and cell reproduction might recover before photosynthesis; most biological functions potentially restarted after ~6 h. Furthermore, we identified novel genes and proteins related to desiccation tolerance in bryophytes. Overall, this study provides new strategies for analyzing desiccation-tolerant bryophytes and identifying candidate genes for improving plant drought tolerance.
... Therefore, the most commonly used plastid markers (i.e. the rps4 gene and trnL-trnF region; cf Stech and Quandt 2010), individually or in combination, are the only useful regions for most groups for which ITS barcoding is not possible, despite their lower barcoding specificity. Creating larger barcoding libraries using other variable plastid regions, such as the trnL-rps4 spacers and the trnK, trnG or rpl16 introns (Liu et al. 2011;Stech et al. 2013;Lang et al. 2014;Wynns and Lange 2014;Valente et al. 2019), might prove to be a better solution in the future. ...
Introduction. We report the results of an international bryological expedition to the Khamar-
Daban mountain range in Russian southern Siberia. The novel approach of integrative floristics
is introduced here as a method of surveying the flora of a region by using a combination of
morphological and molecular evidence to identify and verify unexpected findings. We show
that use of this approach can deliver a high level of credibility in cases in which direct
molecular comparison is possible or the relevant data can be easily obtained from reliable
studies informing recent treatments. Integrative floristics can also be used to identify
potential taxonomic problems requiring further study.
Methods. Conventional identification methods based on plant anatomy and morphology were
supplemented with molecular barcoding (nuclear ITS, plastid trnL–trnF, rps4 and atpB–rbcL
regions) of specimens that either did not fit existing morphological concepts perfectly or for
which records were unexpected based on previously established phytogeographical patterns.
Key results and conclusions. In total, we recorded ca 380 species of mosses and ca 150
species of liverworts from five localities on the northern slopes of the Khamar-Daban range.
Such floristic richness indicates a hotspot of bryophyte diversity with a remarkably high
proportion of suboceanic species, such as Brachydontium trichodes (F.Weber) Milde,
Herzogiella striatella (Brid.) Z.Iwats. and Racomitrium macounii subsp. alpinum (E.Lawton)
Frisvoll. Nearly 20% of specimens were identified or checked using DNA barcoding. This
approach showed the presence of previously unrecorded species in a number of genera,
including Didymodon, Neckera and Pseudohygrohypnum.
... The results have frequently unveiled a remarkable taxonomic diversity (see, e.g. Medina et al., 2012;Stech et al., 2013;Hedenäs et al., 2014;Heinrichs et al., 2015;Carter et al., 2017;Sim-Sim et al., 2017). ...
Orthotrichum lyellii was described in 1878 based on the crisped leaves with plane margins on its elongated and branched stems, and on the presence of brood-bodies. In Europe, these characters remain constant, but in North America several similar forms lacking propagules have been described either at the specific or infraspecific level. These were all reduced to synonyms of O. lyellii. In 2015, Orthotrichum was divided, and O. lyellii was transferred to Pulvigera, a genus thus far considered to be monospecific. In this study, the variability of P. lyellii is analysed in an integrative taxonomic framework. Morphological studies on > 200 specimens, including the nomenclatural types of the taxa previously described, were combined with biogeographical and ecological evidence and with a phylogenetic reconstruction of 39 terminals based on five molecular loci. All the sources of evidence suggest the existence of four different taxa in North America, one also present on the Marquesas Islands. The study of type materials led to their identification as P. lyellii and three other taxa previously described from North America, Orthotrichum papillosum, O. lyellii var. howei and O. pringlei. These taxa differ from each other in taxonomically significant morphological characters of the gametophyte and sporophyte. The morphological diversity has led us to reinterpret Pulvigera, and to amend its description. Nomenclatural changes for the reinstated taxa are proposed, and full descriptions and an identification key for Pulvigera spp. in North America are provided.
... While some studies concluded that it may take several markers to distinguish all species of a bryophyte genus with statistical support (e.g., Arctic Dicranum species; Lang et al., 2014), other studies suggested that a single marker out of a set of markers tested might suffice. For example, ITS was sufficient to distinguish all studied species of the liverwort genus Herbertus (Bell et al., 2012) and the Racomitrium canescens complex of the moss family Grimmiaceae (Stech et al., 2013). Given the different results in different bryophyte lineages, however, testing the variability and utility for species delimitation of commonly used markers still appears necessary for newly studied genera. ...
Species of the moss genus Schlotheimia are often difficult to identify morphologically, because it is necessary to study sporophytic characters and fertile plants are quite rare. In this paper, we aim to infer the potential of trnG-R, trnL-F, and ITS markers to resolve phylogenetic relationships and species delimitations within Schlotheimia in Brazil, using different tree-based analysis methods and Automatic Barcode Gap Discovery (ABGD). For the first time in bryophytes, the trnG-R spacer was sequenced together with the trnG intron (trnG-R region). Furthermore, we aim to evaluate the morphological species concept based on the molecular data, to aid the on-going taxonomic revision of Schlotheimia in Brazil. The combined analysis of all three markers resolved 11 clades corresponding to Schlotheimia species, which was corroborated by ABGD and morphological characters. The best candidate marker for DNA barcoding was trnG-R due to its easy amplification and ability to discriminate all but one species. While trnG-R is sufficient for routine identification, the combination trnG-R + ITS should be used if all Brazilian Schlotheimia species are to be identified with high statistical support. The nuclear marker ITS was easy to amplify and more variable than the plastid markers, but a higher percentage of low quality sequences due to polynucleotide stretches or fungal contamination is a potential drawback. TrnL-F had a low discrimination potential. The analysis of the molecular markers investigated provides a baseline for the taxonomic revision of Schlotheimia and is an important tool for the identification of sterile specimens.
... Désamoré et al., 2016;Kyrkjeeide et al., 2016;Ledent et al., 2019) raises the question whether patterns of species richness and distribution in traditionally defined bryophyte species truly characterize the lack of intercontinental geographic barriers or rather reflect taxonomical shortcomings. In fact, an increasing number of studies have reported that apparently widely distributed bryophyte species correspond to complexes of multiple, not necessarily sister species with much narrower distribution ranges ( Heinrichs et al., 2010;Stech et al., 2013;Lang et al., 2015;Carter et al., 2017). ...
... According to the results, it surpassed the resolution of the ITS2 region, both alone and in combination with other barcodes. The ITS1 region provided better species discrimination than ITS2 and ITS1 + 2 in the study of mosses of the Racomitrium canescens complex (Stech et al., 2013) and the group of legume plants from the subtribe Cassiinae (Mishra et al., 2016). Thus, the usability of marker regions, even with an equal rate and character of their evolution, may vary depending on the task of the study. ...
