To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS:We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS:Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed.CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a sample of 150 phylogenies (12,512 species) of seed plants and tetrapods, and assess their variation across Neotropical regions and taxa. Analyses indicate that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity account for 21% and 9% of Neotropical diversity, respectively. Five biogeographic areas are identified as distinctive units of long-term Neotropical evolution, including Pan-Amazonia, the Dry Diagonal, and Bahama-Antilles. Diversification dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with past climate changes.

abstract. Campylocentrum palominoi, a new species from the western Cordillera of the Andes, department of Valle del Cauca (Colombia), is described and illustrated. This species is similar to C. brenesii, from which it differs mainly by the subequal, ovate, obtuse lobes of the 3-veined lip, abscense of papillae at the middle lobe and the saccate spur which is widened towards the apex.rEsuMEn. Se describe e ilustra a Campylocentrum palominoi, una nueva especie de la Cordillera occidental de los Andes, departamento del Valle del Cauca (Colombia). Esta especie es similar a C. brenesii, de la cual difiere principalmente por los lóbulos laterales del labelo obtusos, ovados, subiguales, lóbulo medio sin papilas en la lámina y por el nectario sacciforme, angosto en la base y ancho en el ápice.

Malaxis nana C. Schweinf. se conoce de dos especímenes recolectados en 1925 en San Ramón, provincia de Alajuela, y tres especímenes adicionales sin datos de localidad detallados y recolectados en los finales de los 1800’s, todos de Costa Rica. Esta especie no había sido registrada desde entonces. Aquí informamos por vez primera sobre la existencia de Malaxis nana en la Estación Biológica Las Cruces, provincia de Puntarenas, en el sur de Costa Rica. Se presenta una descripción actualizada, ilustración, fotografías y mapa de distribución para este taxón.

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Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci, as well as various other biological phenomena responsible for topological incongruence such as ILS and hybridization. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. The complex includes seven taxa distributed in Central America and the adjacent Chocó biogeographic region, nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from a handful of loci failed to provide support for internal relationships within the complex. Our Neighbor-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches species provided a robustly supported network. The resulting three main clades are corroborated by morphological traits and geographical distributions. Similarly, Maximum Likelihood (ML) inferences of concatenated GBS-loci produced results comparable with those derived from coalescence and network-based methods, albeit always with poor statistical support. The low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species might actually represent only three distinct segregates. Our study is the first to demonstrate the utility of GBS data in phylogenomic research of a very young Neotropical plant clade (~2 Ma), and it paves the way for the study of the many other species complexes that populate the species-rich orchid family.

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci, as well as various other biological phenomena responsible for topological incongruence such as ILS and hybridization. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. The complex includes seven taxa distributed in Central America and the adjacent Chocó biogeographic region, nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from a handful of loci failed to provide support for internal relationships within the complex. Our Neighbor-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches species provided a robustly supported network. The resulting three main clades are corroborated by morphological traits and geographical distributions. Similarly, Maximum Likelihood (ML) inferences of concatenated GBS-loci produced results comparable with those derived from coalescence and network-based methods, albeit always with poor statistical support. The low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species might actually represent only three distinct segregates. Our study is the first to demonstrate the utility of GBS data in phylogenomic research of a very young Neotropical plant clade (~2 Ma), and it paves the way for the study of the many other species complexes that populate the species-rich orchid family.

No abstract