Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

PREMISE OF THE STUDY

We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification.

METHODS

We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth.

KEY RESULTS

Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches.

CONCLUSIONS

We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).

Building the monocot tree of death: Progress and challenges emerging from the macrofossil-rich Zingiberales

PREMISE OF THE STUDY

Inclusion of fossils in phylogenetic analyses is necessary in order to construct a comprehensive "tree of death" and elucidate evolutionary history of taxa; however, such incorporation of fossils in phylogenetic reconstruction is dependent on the availability and interpretation of extensive morphological data. Here, the Zingiberales, whose familial relationships have been difficult to resolve with high support, are used as a case study to illustrate the importance of including fossil taxa in systematic studies.

METHODS

Eight fossil taxa and 43 extant Zingiberales were coded for 39 morphological seed characters, and these data were concatenated with previously published molecular sequence data for analysis in the program MrBayes.

KEY RESULTS

Ensete oregonense is confirmed to be part of Musaceae, and the other seven fossils group with Zingiberaceae. There is strong support for Spirematospermum friedrichii, Spirematospermum sp. 'Goth', S. wetzleri, and Striatornata sanantoniensis in crown Zingiberaceae while "Musa" cardiosperma, Spirematospermum chandlerae, and Tricostatocarpon silvapinedae are best considered stem Zingiberaceae. Inclusion of fossils explains how different topologies from morphological and molecular data sets is due to shared plesiomorphic characters shared by Musaceae, Zingiberaceae, and Costaceae, and most of the fossils.

CONCLUSIONS

Inclusion of eight fossil taxa expands the Zingiberales tree and helps explain the difficulty in resolving relationships. Inclusion of fossils was possible in part due to a large morphological data set built using nondestructive microcomputed tomography data. Collaboration between paleo- and neobotanists and technology such as microcomputed tomography will help to build the tree of death and ultimately improve our understanding of the evolutionary history of monocots.

Orchid phylogenomics and multiple drivers of their extraordinary diversification

Orchids are the most diverse family of angiosperms, with over 25 000 species,more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here,we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. Asupermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras),and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp(-1) My(-1)) is 6.8 times that at the Asparagales crown.

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

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.

Molecular phylogenetics of Hydatellaceae (Nymphaeales): sexual-system homoplasy and a new sectional classification

PREMISE OF THE STUDY

Species relationships are unknown in Hydatellaceae, a small family of dwarf aquatics related to water lilies that arose near the base of angiosperm phylogeny. Here we use molecular evidence to infer a species tree for the family and apply this to reconstructing major transitions in morphology and sexual system in this early branch of angiosperms.

METHODS

We assembled plastid (atpB, matK, ndhF, rbcL) and nuclear (ribosomal ITS) data for 50 samples (including outgroups) and estimated a species tree for Hydatellaceae using a Bayesian multispecies coalescent approach. We reconstructed the evolution of several morphological characters, then tested for associations between sexual system and reproductive morphology using phylogenetic ANOVA.

KEY RESULTS

Dioecious species of Hydatellaceae have significantly greater stamen number and anther length than do cosexual species, suggesting changes in male function. The perennial habit that defines one subclade likely represents a reversion from annuality. Species relationships do not fall along traditional morphological divisions, but new sections proposed here are supported by fruit and seed synapomorphies. The earliest split in the family is reflected in geography and climate (i.e., tropical vs. subtropical/temperate clades). We found limited evidence of incongruence between plastid and nuclear trees, with one exception involving gene-tree nonmonophyly for two close relatives (Trithuria submersa, T. bibracteata).

CONCLUSIONS

While the direction of sexual-system evolution is ambiguous, transitions are significantly associated with changes in involucral phyllome length and proxies of pollen production. We propose a new sectional circumscription based on fruit, seed, and DNA evidence.

Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny

We examined multiple plastid genes from a diversity of gymnosperm lineages to explore the consistency of signal among different outgroups for rooting flowering plant phylogeny. For maximum parsimony (MP), most outgroups attach on a branch of the underlying ingroup tree that leads to Amborella. Maximum likelihood (ML) analyses either root angiosperms on a nearby branch or find split support for these neighboring root placements, depending on the outgroup. The inclusion of two species of Hydatellaceae, recently recognized as an ancient line of angiosperms, does not aid in inference of the root. Cost profiles for placing the root in suboptimal locations are highly correlated across most outgroup comparisons, even comparing MP and ML profiles. Those for Gnetales are the most deviant of all those considered. This divergent outgroup either attaches on a long eudicot branch with moderate bootstrap support in MP analyses or supports no particular root location in ML analysis. Removing the most rapidly evolving sites in rate classifications based on two divergent angiosperm root placements with Gnetales yields strongly conflicting root placements in MP analysis, despite substantial overlap in the estimated sets of conservative sites. However, the generally high consistency in rooting signal among distantly related gymnosperm clades suggests that the long branch connecting angiosperms to their extant relatives may not interfere substantially with inference of the angiosperm root.