Background Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species. Results The results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9–37.0%. Gene annotation revealed 106–109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust. Conclusions Our study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.

The research about species richness pattern and elevational Rapoport's rule (ERR) have been carried out mostly in the temperate regions in the recent years and scarcely in the tropical mountains; meanwhile, it is unclear whether the ERR is consistent among different life‐forms and phytogeographic affinities. Here, we compiled a database of plant species of Mount Kenya, a tropical mountain of East Africa, and divided these species into twelve groups depending on the life‐form and phytogeographic affinity of each species. We inspected the species richness pattern of each group along the elevation gradient and also tested ERR of each group using Stevens' method. Our results showed that species richness of the total species showed a positively skewed (hump‐shaped) pattern along the elevation gradient and different life‐forms and phytogeographic affinities showed similar hump‐shaped patterns as the total species. The average elevation range size of the total species and herbaceous species showed increasing patterns along the elevation gradient, while lycophytes and ferns, and woody species showed an obvious downward trend after peaking in the high elevation regions. We concluded that the widely distributed herbaceous species which also have broad elevation range sizes are more applicable to ERR, while the narrowly distributed woody species with small elevation range sizes occurring in the higher elevations could reverse ERR. Therefore, we concluded that the ERR is not consistent among different organisms in the same region.

Mount Kenya is of ecological importance in tropical east Africa due to the dramatic gradient in vegetation types that can be observed from low to high elevation zones. However, species richness and phylogenetic diversity of this mountain have not been well studied. Here, we surveyed distribution patterns for a total of 1,335 seed plants of this mountain and calculated species richness and phylogenetic diversity across seven vegetation zones. We also measured phylogenetic structure using the net relatedness index (NRI) and the nearest species index (NTI). Our results show that lower montane wet forest has the highest level of species richness, density, and phylogenetic diversity of woody plants, while lower montane dry forest has the highest level of species richness, density, and phylogenetic diversity in herbaceous plants. In total plants, NRI and NTI of four forest zones were smaller than three alpine zones. In woody plants, lower montane wet forest and upper montane forest have overdispersed phylogenetic structures. In herbaceous plants, NRI of Afro‐alpine zone and nival zone are smaller than those of bamboo zone, upper montane forest, and heath zone. We suggest that compared to open dry forest, humid forest has fewer herbaceous plants because of the closed canopy of woody plants. Woody plants may have climate‐dominated niches, whereas herbaceous plants may have edaphic and microhabitat‐dominated niches. We also proposed lower and upper montane forests with high species richness or overdispersed phylogenetic structures as the priority areas in conservation of Mount Kenya and other high mountains in the Eastern Afro‐montane biodiversity hotspot regions.

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Interactions within lichen communities include, in addition to close mutualistic associations between the main partners of specific lichen symbioses, also more elusive relationships between members of a wider symbiotic community. Here, we analyze association patterns of cyanolichen symbionts in the tropical montane forests of Taita Hills, southern Kenya, which is part of the Eastern Afromontane biodiversity hotspot. The cyanolichen specimens analyzed represent 74 mycobiont taxa within the order Peltigerales (Ascomycota), associating with 115 different variants of the photobionts genus Nostoc (Cyanobacteria). Our analysis demonstrates wide sharing of photobionts and reveals the presence of several photobiont-mediated lichen guilds. Over half of all mycobionts share photobionts with other fungal species, often from different genera or even families, while some others are strict specialists and exclusively associate with a single photobiont variant. The most extensive symbiont network involves 24 different fungal species from five genera associating with 38 Nostoc photobionts. The Nostoc photobionts belong to two main groups, the Nephroma-type Nostoc and the Collema/Peltigera-type Nostoc, and nearly all mycobionts associate only with variants of one group. Among the mycobionts, species that produce cephalodia and those without symbiotic propagules tend to be most promiscuous in photobiont choice. The extent of photobiont sharing and the structure of interaction networks differ dramatically between the two major photobiont-mediated guilds, being both more prevalent and nested among Nephroma guild fungi and more compartmentalized among Peltigera guild fungi. This presumably reflects differences in the ecological characteristics and/or requirements of the two main groups of photobionts. The same two groups of Nostoc have previously been identified from many lichens in various lichen-rich ecosystems in different parts of the world, indicating that photobiont sharing between fungal species is an integral part of lichen ecology globally. In many cases, symbiotically dispersing lichens can facilitate the dispersal of sexually reproducing species, promoting establishment and adaptation into new and marginal habitats and thus driving evolutionary diversification.