We use multiple photosynthetic, chlororespiratory, and plastid translation apparatus loci and their associated noncoding regions (ca. 16 kb per taxon, prior to alignment) to make strongly supported inferences of the deep internal branches of monocot phylogeny. Most monocot relationships are robust (an average of ca. 91 % bootstrap support per branch examined), including those poorly supported or unresolved in other studies. Our data strongly support a sister-group relationship between Asparagales and the commelinid monocots, the inclusion of the orchids in Asparagales, and the status of Petrosaviaceae as the sister group of all monocots except Acarus and Alismatales. The latter finding supports recognition of the order Petrosaviales. Also strongly supported is a placement of Petermannia disjunct from Colchicaceae (Liliales) and a sister-group relationship between Commelinales and Zingiberales. We highlight the remaining weak areas of monocot phylogeny, including the positions of Dioscoreales, Liliales, and Pandanales. Despite substantial variation in the overall rate of molecular evolution among lineages, inferred amounts of change among codon-position data partitions are correlated with each other across the monocot tree, consistent with low incongruence between these partitions. Ceratophyllum and Chloranthaceae appear to have a destabilizing effect on the position of the monocots among other angiosperms; the issue of monocot placement in broader angiosperm phylogeny remains problematic.

No abstract

Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.

Recent re-examinations and new fossil findings have added significantly to the data available for evaluating the evolutionary history of the monocotyledons. Integrating data from the monocot fossil record with molecular dating techniques has the potential to help us to understand better the timing of important evolutionary events and patterns of diversification and extinction in this major and ancient clade of flowering plants. In general, the oldest well-placed fossils are used to constrain the age of nodes in molecular dating analyses. However, substantial error can be introduced if calibration fossils are not carefully evaluated and selected. Here we propose a set of 34 fossils representing 19 families and eight orders for calibrating the ages of major monocot clades. We selected these fossils because they can be placed in particular clades with confidence and they come from well-dated stratigraphic sequences. As more fossils are discovered or re-examined, these criteria can also be applied to expand the list of the fossils that are most suitable for dating the early branches of monocot phylogeny.