The classification of species-rich genera is one of the most challenging tasks in systematics. In this paper we present an updated infrageneric classification of the genus Peperomia (Piperaceae), one of the most species-rich genera of plants. The classification is based on a molecular phylogeny of 190 accessions and the placement of 1340 of the 1606 currently accepted taxa within this classification. We provide the most comprehensive circumscriptions of Peperomia subgenera since the work of Dahlstedt in 1900, with five newly described subgenera. Fourteen monophyletic groups were revealed by phylogenetic reconstructions, including two newly discovered clades. Extensive field work, monitoring of representative living collections in our botanical gardens, and herbarium studies were the basis for morphological assignment of 80% of Peperomia species to the subgenera recognized and described herein. This work, in combination with the detailed descriptions of these subgenera, will aid field botanists, taxonomists, and ecologists to properly collect and identify species. Although parallel evolution of characters makes identification of species within Peperomia difficult, especially in species-rich clades, the key to subgenera will provide a useful framework for anyone interested in this genus and will be a reference for further studies in Peperomia.

Aim Isotrema is a monophyletic subgenus of Aristolochia with species in East Asia and North/Central America. Earlier studies, based on limited sampling, suggested that the Asian and American species do not form two reciprocal sister clades. We reconstructed phylogenetic relationships within Isotrema to infer the biogeographical events that have shaped its present-day distribution.Location Eastern Asia, North America, Mexico, Central America.Methods We performed parsimony and Bayesian phylogenetic analyses of 54 accessions using three chloroplast regions. The temporal origins were traced with relaxed phylogenetics and penalized likelihood using fossil calibrations; these methods were combined with ancestral area reconstructions in a comparative approach using statistical dispersal-vicariance analysis (S-DIVA) and dispersal-extinction-cladogenesis (DEC) analyses.Results The ancestors of the herbaceous eastern North American species and the woody species probably diverged during the Oligocene. The woody species form a Neotropical and a North American/Eastern Asian clade. Diversification in the Neotropical and North American/Eastern Asian clades occurred mostly in the Miocene. In the latter clade, two further intercontinental splits are reconstructed: between the exclusively western North American Aristolochia californica and most of the Asian taxa, and between A. manshuriensis and A. tomentosa.Main conclusions The present distribution of Isotrema developed via a number of dispersal, vicariance and extinction events. The disjunct distributions observed may be the result mainly of non-synchronous events (e. g. a decrease of mean annual temperature in the Oligocene and the development of unfavourable conditions across the Bering land bridge) that were responsible for the fragmentation of the mesophytic forests. Later diversifications may be correlated with events such as the orogeny of the Western Cordillera and Appalachian Mountains, the development of extensive grasslands in North America, and the mainland extension of Central America southwards to western and central Panama.

Recent phylogenetic analyses challenged the traditional generic concept of the Bartramiaceae (apple mosses), especially with regard to the largest genus Bartramia . Although molecular analyses revealed the three Bartramia sections ( Bartramia , Strictidium and Vaginella ) to be monophyletic, they appeared in different parts of the inferred phylogenies and thus rendered the genus itself polyphyletic. In addition, Anacolia laevisphaera , a tropical montane species, appeared in the section Strictidium , weakening its character as a typical Mediterranean element. Although morphologically similar to members of the section, such as B. stricta , A. laevisphaera has been generally treated within the genus Anacolia based on sporophytic characters. In fact, Anacolia laevisphaera is often confused with B. stricta in sterile condition. A thorough analysis revealed another surprise, in placing A. laevisphaera sister to the Southern South American samples of Bartramia stricta, while the Mediterranean populations of “ B. stricta ” cluster with the Australian B. breutelii . Subsequent morphometric studies revealed three morpho-species in accordance with the polyphyletically resolved B. stricta . Here we describe the new species Bartramia rosamrosiae to accommodate the Mediterranean and western North American populations of what was traditionally treated as B. stricta .

Aim Peperomia subgenus Tildenia consists of c. 60 species growing in seasonal habitats of Neotropical mountain areas from Mexico to Argentina. The subgenus can be split geographically, with almost equal diversity in the Northern Hemisphere (centred in Mexico and Guatemala) and in the Southern Hemisphere (centred in Peru and Bolivia). Only a few species are known from a limited number of localities between these two hotspots. As such, Tildenia is an ideal candidate with which to test time, direction and mode of migration of high mountain taxa against the background of the Great American Biotic Interchange.Location The Andes with focus on the Central Andes, and the Mexican mountain chains, especially the Trans-Mexican Volcanic Belt.Methods To elucidate the spatio-temporal origin, subsequent colonization and radiation of Tildenia, we combine Bayesian phylogenetics based on the chloroplast trnK-matK-psbA region, georeferenced distribution data, and fossil calibrated molecular dating approaches using both penalized likelihood and relaxed phylogenetics. Reconstruction of the ancestral distribution area was performed using dispersal-vicariance analysis and dispersal-extinction-cladogenesis.Results Peperomia subgenus Tildenia is subdivided into six Andean clades and one Mexican and Central American clade originating from a north/central Peruvian ancestor. Molecular dating approaches converge on a stem age of c. 38 Ma for Tildenia and a mostly Miocene diversification and colonization.Main conclusions We detect a strong correlation between diversification of Tildenia and orogenetic events in the respective distribution centres. In the Andes, distribution was influenced by the Altiplano-Eastern Cordillera System as well as the Amotape-Huancabamba Zone, where the latter serves as both migration barrier and migration bridge for different clades. In contrast to most studies of high-elevation taxa, we provide support for a south-north colonization towards Central America and Mexico, and provide additional, independent evidence for the latest view on the timing of the Great American Biotic Interchange. In Mexico, the Trans-Mexican Volcanic Belt has played a major role in more recent radiations together with climatic oscillation and the formation of refugia.

Peperomia subgénero Tildenia es un grupo poco conocido de especies geofíticas de hábitats estacionales en 2 hotspots de biodiversidad (México-Guatemala y Perú-Bolivia) con pocas especies en los países de enmedio. El trabajo de campo realizado recientemente en México y América Central, combinado con un estudio detallado de ejemplares de herbario de este subgénero, resultó en el descubrimiento de 12 especies nuevas, que se describen e ilustran. Además, una variedad anteriormente publicada es elevada a la categoría de especie. Se incluyen datos de distribución, hábitat y fenología, comparaciones detalladas con otras especies, así como una clave de identificación para todas las especies del subgénero en la región estudiada.

BACKGROUND:The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, agt1, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose Tildenia, a subgenus of Peperomia (Piperaceae), one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, Tildenia is a perfect test case for applying new phylogenetic tools.RESULTS:We show that the nuclear marker agt1, and in particular the agt1 introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from agt1 intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (trnK intron, trnK-psbA spacer, ndhF-rpl32 spacer, rpl32-trnL spacer, psbA-trnH spacer) provide less than 10% parsimony informative characters. The agt1 dataset provides a deeper resolution than the chloroplast markers in Tildenia.CONCLUSIONS:Single (or very low) copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of taxonomic levels from family down to population level. As more plant genomes are sequenced, we will obtain increasingly precise information about which genes return to single copy most rapidly following gene duplication and may be most useful across a wide range of plant groups.

Peperomia subgenus Tildenia is a poorly known group of geophytic species occurring in seasonal habitats in 2 biodiversity hot spots (Mexico-Guatemala and Peru-Bolivia) with few species reported from the countries in between. Recent fieldwork combined with detailed study of herbarium specimens of this subgenus in Mexico and Central America resulted in the discovery of 12 new species, which are here described and illustrated. In addition, 1 formerly published variety is raised to species rank. Distribution, habitat and phenology data and detailed comparisons with other species are included, as well as an identification key for all species belonging to this subgenus in the studied area.Peperomia subgénero Tildenia es un grupo poco conocido de especies geofíticas de hábitats estacionales en 2 hotspots de biodiversidad (México-Guatemala y Perú-Bolivia) con pocas especies en los países de enmedio. El trabajo de campo realizado recientemente en México y América Central, combinado con un estudio detallado de ejemplares de herbario de este subgénero, resultó en el descubrimiento de 12 especies nuevas, que se describen e ilustran. Además, una variedad anteriormente publicada es elevada a la categoría de especie. Se incluyen datos de distribución, hábitat y fenología, comparaciones detalladas con otras especies, así como una clave de identificación para todas las especies del subgénero en la región estudiada.

Background and aims - The pantropical genus Peperomia consists of approximately 1,600 species with an extremely diverse vegetative morphology, especially in the Neotropics. One of the most startling yet overlooked growth forms is the geophytic one, as in subgenus Tildenia. This group occurs in seasonal Neotropical habitats with its highest diversity in Mexico-Guatemala and Peru-Bolivia with few species known from in between these hot spots.Methods - Recent fieldwork in Peru and Bolivia combined with herbarium study and a Bayesian analysis of an aligned sequence matrix of the chloroplast trnK-matK-psbA gene cluster of one accession of each species resulted in new findings within this subgenus.Key results - Fourteen new species are described, discussed in a phylogenetic framework and illustrated. Two species have a wide distribution and occur from central W. Peru to S. Bolivia: the common P. cerrateae and the rare P. parvisagittata. Three endemic species are described from the Amotape-Huancabamba Zone which is particularly rich in tuberous Peperomia species: P. gigantea, P. jalcaensis and P. klopfensteinii. Two species are only known from their type locality in central W. Peru: P. ocrosensis and P. pugnicaudex. Five other Peruvian species are P. ayacuchoana from Ayacucho, P. querocochana from Ancash, wernerrauhii from Huanuco, Peperomia umbrosa from three distant localities, and P. pseudoverruculosa which is relatively common in SE Peru. Two species are Bolivian endemics: the rare P. purpureonervosa from La Paz and the more common P. radiatinervosa from Cochabamba and Chuquisaca. Two former varieties, both endemics of the extreme northern Central Andes, are raised to species rank: P. lilliputiana and P. pseudoperuviana. Finally, basionym rejection and lectotypification are proposed for the widespread and commonly collected tuberous Peperomia in the southern Central Andes: R peruviana. An emended description of Peperomia subgenus Tildenia is also provided.