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Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract

Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides , and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai’i. The three distinct Hawaiian genera, Haplostachys , Phyllostegia , and Stenogyne , are nested inside a fourth genus, Stachys . We uncovered four independent polyploidy events within Stachys , including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin’s thinking about the evolutionary process. Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage

Lamioideae comprise the second-largest subfamily in Lamiaceae. Although considerable progress has recently been made in Lamioideae phylogenetics, the subfamily remains one of the most poorly investigated subfamilies in Lamiaceae. Here we present a taxonomic update of the subfamily based on earlier published data as well as 71 new DNA extracts from relevant in-and outgroup taxa, and DNA sequence data from four chloroplast regions (matK, rpsl6, trnL intron and trnL-F spacer). The phylogenetic positions of 10 out of 13 previously unplaced small or monotypic Asian lamioid genera and 37 additional lamioid species have been identified, and the classification is updated accordingly. Results from parsimony and Bayesian phylogenetic methods corroborate earlier results, but phylogenetic resolution as well as overall branch support are improved. All newly added genera are assigned to earlier established tribes or the new tribe Paraphlomideae Bendiksby, which includes Ajugoides, Matsumurella and Paraphlomis. Acanthoprasium is resurrected as a genus. Transfer of species is proposed to accommodate the monophyly of two genera (Lamium, Otostegia), whereas ten genera remain non-monophyletic (Ballota s. str., Lagopsis, Leonotis, Leonurus, Leucas, Microtoena, Phlomoides, Sideritis, Stachys, Thuspeinanta). Eriophyton and Stachyopsis have been included in Lamieae, Hypogomphia in Stachydeae, and Loxocalyx in Leonureae. Betonica, Colquhounia, Galeopsis, and Roylea remain unclassified at the tribal level. Lamium chinense and three East Asian Galeobdolon species are transferred to Matsumurella. Sulaimania and four Otostegia species are transferred to Moluccella. Alajja and three Lamium species are transferred to Eriophyton. In total, 14 new combinations are made, one at the rank of subgenus and 13 at the rank of species.

Species occurrence data records the location and time of an encounter with a species, and is valuable for many aspects of ecological and evolutionary analyses. A key distinction within species occurrence data is between (1) collected and preserved specimens that can be taxonomically validated (i.e., natural history collections), and (2) observations, which are more error prone but richer in terms of number and spread of observations. In this study we analyse the distribution in temporal, spatial, taxonomic and environmental coverage of specimen- and observation based species occurrence data for land plants in Norway, a region with strong climatic and human population density gradients. Of 4.8 million species occurrence records, the majority (78%) were observations. However, there was a greater species richness in the specimen record (N = 4691) than in the observation record (N = 3193) and most species were recorded more as specimens than observations. Specimen data was on average older, and collected later during the year. Both record types were highly influenced by a small number of prolific contributors. The species most highly represented in the observation data set were widespread or invasive, while in the specimen records, taxonomically challenging species were overrepresented. Species occurrence records were unevenly spatially distributed. Both specimen and observation records were concentrated in regions of Norway with high human population density and with high temperatures and precipitation, but in different regions within Norway. Observation and specimen records thus differ in taxonomic, temporal, spatial and environmental coverage for a well-sampled group and study region, potentially influencing the ecological inferences made from studies utilizing species occurrence data. The distribution of observation data dominates the dataset, so inferences of species diversity and distributions do not correspond to the evolutionary or physiological knowledge of species, which is based on specimen data. We make recommendations for users of biodiversity data, and collectors to better exploit the complementary strengths of these distinct biodiversity data types.

Background The fungal genus Serpula (Serpulaceae, Boletales) comprises several saprotrophic (brown rot) taxa, including the aggressive house-infecting dry rot fungus Serpula lacrymans . Recent phylogenetic analyses have indicated that the ectomycorrhiza forming genera Austropaxillus and Gymnopaxillus cluster within Serpula . In this study we use DNA sequence data to investigate phylogenetic relationships, historical biogeography of, and nutritional mode transitions in Serpulaceae. Results Our results corroborate that the two ectomycorrhiza-forming genera, Austropaxillus and Gymnopaxillus , form a monophyletic group nested within the saprotrophic genus Serpula , and that the Serpula species S. lacrymans and S. himantioides constitute the sister group to the Austropaxillus - Gymnopaxillus clade. We found that both vicariance (Beringian) and long distance dispersal events are needed to explain the phylogeny and current distributions of taxa within Serpulaceae. Our results also show that the transition from brown rot to mycorrhiza has happened only once in a monophyletic Serpulaceae, probably between 50 and 22 million years before present. Conclusions This study supports the growing understanding that the same geographical barriers that limit plant- and animal dispersal also limit the spread of fungi, as a combination of vicariance and long distance dispersal events are needed to explain the present patterns of distribution in Serpulaceae. Our results verify the transition from brown rot to ECM within Serpulaceae between 50 and 22 MyBP.

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.

The species we have studied the spatiotemporal genetic change in the northern dragonhead, a plant species that has experienced a drastic population decline and habitat loss in Europe. We have added a temporal perspective to the monitoring of northern dragonhead in Norway by genotyping herbarium specimens up to 200 years old. We have also assessed whether northern dragonhead has achieved its potential distribution in Norway. To obtain the genotype data from 130 herbarium specimens collected from 1820 to 2008, mainly from Norway (83) but also beyond (47), we applied a microfluidic array consisting of 96 SNP markers. To assess temporal genetic change, we compared our new genotype data with existing data from modern samples. We used sample metadata and observational records to model the species' environmental niche and potential distribution in Norway. Our results show that the SNP array successfully genotyped all included herbarium specimens. Hence, with the appropriate design procedures, the SNP array technology appears highly promising for genotyping old herbarium specimens. The captured genetic diversity correlates negatively with distance from Norway. The historical‐modern comparisons reveal similar genetic structure and diversity across space and limited genetic change through time in Norway, providing no signs of any regional bottleneck (i.e., spatiotemporal stasis). The regional areas in Norway have remained genetically divergent, however, both from each other and more so from populations outside of Norway, rendering continued protection of the species in Norway relevant. The ENM results suggest that northern dragonhead has not fully achieved its potential distribution in Norway and corroborate that the species is anchored in warmer and drier habitats. Our study provides new insight to guide conservation priorities for the charismatic flowering plant called northern dragonhead (Dracocephalum ruyschiana). It also showcases a fruitful integration of methods and data sources that jointly enables a holistic species assessment covering space and time.

ABSTRACTWe report here the draft de novo genome assembly, transcriptome assembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument.

We have addressed phylogenetic relationships and tested hypotheses about five presumed subgroups among 15 species of Hypocenomyce s.l. (including Pycnora) by use of nuclear (ITS, LSU) and mitochondrial (SSU) ribosomal DNA‐regions. Bayesian, likelihood and parsimony phylogenetic analyses, of a dataset with broad Lecanoromycete taxon sampling, mostly support the five presumed subgroups, but two of these were found to be polyphyletic (the H. friesii‐group and Pycnora). The seven supported Hypocenomyce s.l. clades belong in different genera, families, orders and even subclasses, and represent a remarkable example of morphological and ecological convergence. Based on our molecular phylogenetic results, we split Hypocenomyce into four genera placed in two subclasses: (1) Carbonicola gen. nov. (Carbonicolaceae fam. nov., Lecanorales, Lecanoromycetidae; including C. anthracophila comb. nov., C. foveata comb. nov., and C. myrmecina comb. nov.); (2) Fulgidea gen. nov. (Umbilicariaceae, Umbilicariales, Umbilicariomycetidae subcl. nov.; including F. oligospora comb. nov. and F. sierrae comb. nov.); (3) Hypocenomyce (Ophioparmaceae, Umbilicariales; including H. australis, H. scalaris, and H. tinderryensis; and (4) Xylopsora gen. nov. (Umbilicariaceae; including X. caradocensis comb. nov. and X. friesii comb. nov.). We split Pycnora into two genera: (1) Pycnora (Pycnoraceae fam. nov., Candelariales, \"Candelariomycetidae\"; including P. praestabilis, P. sorophora, and P. xanthococca); and (2) Toensbergia gen. nov. (Sporastatiaceae fam. nov., unknown order, Lecanoromycetidae; including T. leucococca comb. nov.). We place Hypocenomyce isidiosa in Xylographa (Trapeliaceae, Baeomycetales, Ostropomycetidae; X. isidiosa comb. nov.). We place the family Ophioparmaceae in the Umbilicariales. Our type studies have shown that the epithet “myrmecina” should replace “castaneocinerea”, and lectotypes are chosen for Lecidea friesii Ach., L. scalaris var. myrmecina Ach., Psora cladonioides var. albocervina Räsänen, and P. cladonioides var. castaneocinerea Räsänen. Elixia cretica is reported as new to North America (from Mexico) and Australia.

The Ramalinaceae is the fourth-largest family of lichenized ascomycetes with 42 genera and 913 species exhibiting considerable morphological variation. Historically, generic boundaries in the Ramalinaceae were primarily based on morphological characters. However, molecular systematic investigations of subgroups revealed that current taxonomy is at odds with evolutionary relationships. Tropical members of the family remain particularly understudied, including the large genus Phyllopsora. We have generated and collected multilocus sequence data (mtSSU, nrITS, nrLSU, RPB1, RPB2) for 149 species associated with the Ramalinaceae and present the first comprehensive molecular phylogeny of the family. We used ancestral state reconstructions on our molecular family phylogeny to trace the evolution of character states. Our results indicate that the Ramalinaceae have arisen from an ancestor with long, multiseptate ascospores living in humid temperate forests, and that the phyllopsoroid growth form has evolved multiple times within the family. Based on our results using integrative taxonomy, we discuss sister-relations and taxon-delimitation within five well-supported clades: The Bacidia, Biatora-, Ramalina-, Rolfidium-, and Toninia-groups. We reduce six genera into synonymy and make 49 new nomenclatural combinations. The genera Bacidia, Phyllopsora, Physcidia and Toninia are polyphyletic and herein split into segregates. We describe the two genera Bellicidia and Parallopsora and resurrect the genera Bibbya, Kiliasia, Sporacestra, and Thalloidima. According to our new circumscription, which also includes some additional changes, the family Ramalinaceae now comprises 39 genera.