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Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.]

 

A new species of blueberry, Vaccinium coarctatum M.N.Tamayo & Fernando, from the dwarf forest on ultramafic soil of Dinagat Island, Philippines, is described. It closely resembles Vaccinium hamiguitanense P.W.Fritsch but is distinct from that species in having a longer inflorescence, shorter pedicels, longer and persistent bracteoles, white-hirsutulous calyx lobes, and shorter anther spurs. This discovery brings the number of Vaccinium species known from the Philippines to 41. A key to the small-leaved Vaccinium in the Philippines is provided. 

Two new species of Vaccinium from the Philippines are described and illustrated from historical herbarium collections. Vaccinium burburan from Luzon Island, Northern Philippines is morphologically similar to V. tenuipes, but is distinguished by having shorter petioles, pedicels and corolla, adaxially pubescent leaf blades with cordate base, apically pubescent corollas, and pubescent filaments throughout. It is only one of two species of Vaccinium in the Philippines known to have a cordate leaf blade base. Vaccinium burburan is considered critically endangered. Vaccinium jubatum from Mindanao Island, Southern Philippines, is morphologically similar to V. sylvaticum, but is distinguished by having a dentate leaf blade margin, shorter inflorescences and pedicels, a glabrous calyx, and shorter filaments. The dentate leaf blade margin of V. jubatum uniquely distinguishes it from other Philippine Vaccinium species. The conservation status of V. jubatum is considered data deficient. These discoveries further increase the current number of known Vaccinium species in the Philippines to 40. 

A new species of Cyne (Loranthaceae) from Bucas Grande and Dinagat Islands, Philippines is described and named C. barcelonae in honor of the Filipina botanist Julie F. Barcelona. Phylogenetic analysis using the complete nuclear ribosomal DNA cistron confirms it is sister to C. banahaensis, the only species among the six in the genus with complete descriptions of floral morphology. The species is similar to the rare C. perfoliata of Papua New Guinea by having connate-perfoliate upper leaves but differs from others in the genus by possessing palmate leaf venation, inflorescences lacking an operculum, light green corollas, and stamens with filaments. No type material for Cyne quadriangula exists, thus this taxon is only known from the original protologue. It was rediscovered on Bucas Grande Island and that collection was described and used as the neotype for the species. A revised description of the genus and key to the seven species is provided. 

Vaccinium carmesinum is described as a new species of Ericaceae from Mt. Tago Range, Mindanao Island, Philippines. It is similar to V. platyphyllum Merrill and V. luzoniense S.Vidal but is distinct from the former by longer and wider leaves, longer racemes, longer bracts, glabrous corollas, and glabrescent fruits, and from the latter by longer petioles, leaf glands distributed along the blade margin, glabrous rachis, and lanate filaments. Vaccinium carmesinum bears the widest leaves among Philippine Vaccinium. Its discovery increases the number of Vaccinium species recognized in the Philippines to 37. 

Vaccinium paradoxum is described as a new species of blueberry from the lowland ultrabasic forest of Northern Sierra Madre Natural Park, Luzon Island, Philippines. It resembles V. halconense, but differs by having shorter inflorescences, fewer flowers per inflorescence, a glabrous inner surface of the corolla, absence of anther spurs, and a glabrous style. Vaccinium paradoxum is unique among the currently known blueberries in Malesia by the presence of sessile glands borne on the pedicel and predominantly near the centre or scattered on the calyx lobes. It is also the only known Philippine Vaccinium to inhabit lowland ultrabasic forest on sea cliffs. 

Vaccinium exiguum from the ultramafic summit of Mt. Victoria, Palawan Island, Philippines is here described as a new species of Ericaceae. It closely resembles V. hamiguitanense but is distinct by having much shorter petioles and leaves, longer and glabrous calyx lobes with serrate lobe margins, a larger corolla with deeper sulcations, and longer stamens with spurs oriented laterally. Vaccinium exiguum represents the third Vaccinium species found on the Island of Palawan and 36 th in the Philippines. 

Hypericum perryongii, from Mindanao Island, Philippines, is herein described and illustrated. This new taxon closely resembles both H. geminiflorum and H. formosanum but can be easily distinguished from the former by its larger corolla and calyx lobes and higher number of stamens per fascicle, and from the latter by its terminally 1-flowered inflorescences and the subsessile and abaxially glaucous leaves. 

Vaccinium hamiguitanense, a new species from the Philippines, is described and illustrated. The new species is most similar to V. gitingense Hook. f. but differs by having smaller leaf blades, leaf blade margins with 2 to 4 impressed more or less evenly distributed crenations (glands) per side, inflorescences with fewer flowers, shorter pedicels that are puberulent and muriculate, and a glabrous floral disk. The new species is endemic to Mt. Hamiguitan Range Wildlife Sanctuary in Davao Oriental Province of Mindanao Island in Tropical Upper Montane Rain Forest and low (“bonsai”) forest on clay derived from ultramafic rock. We assign an IUCN Red List preliminary status as Data Deficient.