An annotated plant checklist of the transboundary volcanic Mt Elgon, East Africa

Mt Elgon is an ancient transboundary volcanic mountain found at the Kenya-Uganda boarder possessing high plant diversity. This study documents an updated checklist of the mountain's vascular plants obtained through random-walk field excursions and retrieval of herbarium specimen tracing back to 1900. We compiled 1709 species from 673 genera in 131 families. One new species of the family Cucurbitaceae was also reported. This checklist records respective habitat, habits, elevation ranges, voucher numbers and global distribution ranges of each species. Native and exotic species were also distinguished, where 8.4% of the total species in 49 families were exotic species. There were 103 endemic species, while 14 species were found to be both rare and endemic. IUCN conservation status revealed 2 Critically Endangered, 4 Endangered, 9 Vulnerable and 2 Near Threatened species. This study presents the first and most comprehensive plant inventory of Mt Elgon that will facilitate further ecological and phylogenetic studies.

Diversity of Leptogium (Collemataceae, Ascomycota) in East African Montane Ecosystems

Tropical mountains and especially their forests are hot spots of biodiversity threatened by human population pressure and climate change. The diversity of lichens in tropical Africa is especially poorly known. Here we use the mtSSU and nuITS molecular markers together with morphology and ecology to assess Leptogium (Peltigerales, Ascomycota) diversity in the tropical mountains of Taita Hills and Mt. Kasigau in Kenya and Mt. Kilimanjaro in Tanzania. The sampled habitats cover a wide range of ecosystems from savanna to alpine heath vegetation and from relatively natural forests to agricultural environments and plantation forests. We demonstrate that Leptogium diversity in Africa is much higher than previously known and provide preliminary data on over 70 putative species, including nine established species previously known from the area and over 60 phylogenetically, morphologically, and/or ecologically defined Operational Taxonomic Units (OTUs). Many traditional species concepts are shown to represent morphotypes comprised of several taxa. Many of the species were only found from specific ecosystems and/or restricted habitats and are thus threatened by ongoing habitat fragmentation and degradation of the natural environment. Our results emphasize the importance of molecular markers in species inventories of highly diverse organism groups and geographical areas.

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.

Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): An impetus for developing an integrated taxonomy

Lichens provide valuable systems for studying symbiotic interactions. In lichens, these interactions are frequently described in terms of availability, selectivity and specificity of the mycobionts and photobionts towards one another. The lichen-forming, green algal genus Trebouxia Puymaly is among the most widespread photobiont, associating with a broad range of lichen-forming fungi. To date, 29 species have been described, but studies consistently indicate that the vast majority of species-level lineages still lack formal description, and new, previously unrecognized lineages are frequently reported. To reappraise the diversity and the evolutionary relationships of species-level lineages in Trebouxia, we assembled DNA sequence data from over 1600 specimens, compiled from a range of sequences from previously published studies, axenic algal cultures, and lichens collected from poorly sampled regions. From these samples, we selected representatives of the currently known genetic diversity in the lichenized Trebouxia and inferred a phylogeny from multi-locus sequence data (ITS, rbcL, cox2). We demonstrate that the current formally described species woefully underrepresent overall species-level diversity in this important lichen-forming algal genus. We anticipate that an integrative taxonomic approach, incorporating morphological and physiological data from axenic cultures with genetic data, will be required to establish a robust, comprehensive taxonomy for Trebouxia. The data presented here provide an important impetus and reference dataset for more reliably characterizing diversity in lichenized algae and in using lichens to investigate the evolution of symbioses and holobionts.

Circumscription of the genus Lepra, a recently resurrected genus to accommodate the "Variolaria"-group of Pertusaria sensu lato (Pertusariales, Ascomycota)

Pertusarialean lichens include more than 300 species belonging to several independent phylogenetic lineages. Only some of these phylogenetic clades have been comprehensively sampled for molecular data, and formally described as genera. Here we present a taxonomic treatment of a group of pertusarialean lichens formerly known as “Pertusaria amara-group”, “Monomurata-group”, or “Variolaria-group”, which includes widespread and well-known taxa such as P. amara, P. albescens, or P. ophthalmiza. We generated a 6-locus data set with 79 OTUs representing 75 species. The distinction of the Variolaria clade is supported and consequently, the resurrection of the genus Lepra is followed. Thirty-five new combinations into Lepra are proposed and the new species Lepra austropacifica is described from mangroves in the South Pacific. Lepra is circumscribed to include species with disciform ascomata, a weakly to non-amyloid hymenial gel, strongly amyloid asci without clear apical amyloid structures, containing 1 or 2, single-layered, thin-walled ascospores. Chlorinated xanthones are not present, but thamnolic and picrolichenic acids occur frequently, as well as orcinol depsides. Seventy-one species are accepted in the genus. Although the distinction of the genus from Pertusaria is strongly supported, the relationships of Lepra remain unresolved and the genus is tentatively placed in Pertusariales incertae sedis.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.