Wendy B. Zomlefer

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

Abstract The order Poales comprises a substantial portion of plant life (7% of all angiosperms and 33% of monocots) and includes taxa of enormous economic and ecological significance. Molecular and morphological studies over the past two decades, however, leave uncertain many relationships within Poales and among allied commelinid orders. Here we present the results of an initial project by the Monocot AToL (Angiosperm Tree of Life) team on phylogeny and evolution in Poales, using sequence data for 81 plastid genes (exceeding 101 aligned kb) from 83 species of angiosperms. We recovered highly concordant relationships using maximum likelihood (ML) and maximum parsimony (MP), with 98.2% mean ML bootstrap support across monocots. For the first time, ML resolves ties among Poales and other commelinid orders with moderate to strong support. Analyses provide strong support for Bromeliaceae being sister to the rest of Poales; Typhaceae, Rapateaceae, and cyperids (sedges, rushes, and their allies) emerge next along the phylogenetic spine. Graminids (grasses and their allies) and restiids (Restionaceae and its allies) are well supported as sister taxa. MP identifies a xyrid clade (Eriocaulaceae, Mayacaceae, Xyridaceae) sister to cyperids, but ML (with much stronger support) places them as a grade with respect to restiids + graminids. The conflict in resolution between these analyses likely reflects long-branch attraction and highly elevated substitution rates in some Poales. All other familial relationships within the order are strongly supported by both MP and ML analyses. Character-state mapping implies that ancestral Poales lived in sunny, fire-prone, at least seasonally damp/wet, and possibly nutrient-poor sites, and were animal pollinated. Five subsequent shifts to wind pollination—in Typhaceae, cyperids, restiids, Ecdeiocoleaceae, and the vast PACCMAD-BEP clade of grasses—are significantly correlated with shifts to open habitats and small, inconspicuous, unisexual, and nectar-free flowers. Prime ecological movers driving the repeated evolution of wind pollination in Poales appear to include open habitats combined with the high local dominance of conspecific taxa, with the latter resulting from large-scale disturbances, combined with tall plant stature, vigorous vegetative spread, and positive ecological feedback. Reproductive assurance in the absence of reliable animal visitation probably favored wind pollination in annuals and short-statured perennials of Centrolepidaceae in ephemerally wet depressions and windswept alpine sites.

Generic circumscription and relationships in the tribe Melanthieae (Liliales, Melanthiaceae), with emphasis on Zigadenus: evidence from ITS and trnL-F sequence data.

The circumscription and relationships of genera within the tribe Melanthieae (29 representative taxa) were evaluated using parsimony analyses of ITS (nuclear ribosomal) and trnL-F (plastid) DNA sequence data, alone and in combination. Proposed new generic circumscriptions, strongly supported by the tree statistics and topologies in all analyses, are correlated with potential morphological synapomorphies at the proper level of universality. Based on the molecular cladograms, Stenanthium is biphyletic, and the traditional Zigadenus s.l. (sensu lato) is polyphyletic. Amianthium and Schoenocaulon are distinct entities; the Veratrum complex is conservatively treated as one large monophyletic genus (including Melanthium). Although some generic relationships are not highly resolved, the analyses provide strong support for Zigadenus glaberrimus as sister to the rest of the tribe, and Amianthium muscitoxicum as closely related to Veratrum s.l. As a result of these analyses, seven genera (some with novel circumscription) are recognized within the tribe Melanthieae: Amianthium, Anticlea, Schoenocaulon, Stenanthium, Toxicoscordion, Veratrum, and Zigadenus.

A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae

• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes.

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

BACKGROUND AND AIMS Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. METHODS Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support. KEY RESULTS Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies. CONCLUSIONS Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.

An Overview of Veratrum s.l. (Liliales: Melanthiaceae) and an Infrageneric Phylogeny Based on ITS Sequence Data

Abstract A synopsis of Veratrum, including commentary on species and character evolution within the genus, is presented. The circumscription and relationships of infrageneric taxa are evaluated using parsimony analyses of ITS (nuclear ribosomal) DNA sequence data of 26 representative taxa. Proposed new infrageneric circumscriptions, strongly supported by tree statistics and topologies, are correlated with potential morphological synapomorphies at the proper level of universality. Based on our analyses, Veratrum is circumscribed broadly (including Melanthium) and divided into two sections and two subsections (most with novel circumscription). This modified infrageneric classification involves reassignment of Veratrum subgenus Pseudoanticlea as subsection Pseudoanticlea. Although interspecific relationships are not highly resolved, the molecular data provide strong support for placing several species previously of unknown affinities and also validate several generalizations concerning character evolution within Veratrum.

Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica

We present the first phylogenomic analysis of relationships among all ten families of Liliales, based on 75 plastid genes from 35 species in 29 genera, and 97 additional plastomes stratified across angiosperm lineages. We used a supermatrix approach to extend our analysis to 58 of 64 genera of Liliales, and calibrated the resulting phylogeny against 17 fossil dates to produce a new timeline for monocot evolution. Liliales diverged from other monocots 124 Mya and began splitting into separate families 113 Mya. Our data support an Australian origin for Liliales, with close relationships between three pairs of lineages (Corsiaceae/Campynemataceae, Philesiaceae/Ripogonaceae, tribes Alstroemerieae/Luzuriageae) in South America and Australia or New Zealand reflecting teleconnections of these areas via Antarctica. Long‐distance dispersal (LDD) across the Pacific and Tasman Sea led to re‐invasion of New Zealand by two lineages (Luzuriaga, Ripogonum); LDD allowed Campynemanthe to colonize New Caledonia after its submergence until 37 Mya. LDD permitted Colchicaceae to invade East Asia and Africa from Australia, and re‐invade Africa from Australia. Periodic desert greening permitted Gloriosa and Iphigenia to colonize Southeast Asia overland from Africa, and Androcymbium–Colchicum to invade the Mediterranean from South Africa. Melanthiaceae and Liliaceae crossed the Bering land‐bridge several times from the Miocene to the Pleistocene.

Infrageneric phylogeny of Schoenocaulon (Liliales: Melanthiaceae) with clarification of cryptic species based on ITS sequence data and geographical distribution

As currently defined, the 24 species of Schoenocaulon occur in three disjunct areas: north central Florida (one species, S. dubium), southern Peru (portion of the range of S. officinale), and the region from southeastern New Mexico-Texas south to Venezuela; the 20 species endemic to Mexico are geographically restricted. Species delimitations, often based on tepal morphology, have been problematic. Our analyses of ITS sequence data for all 27 species and infraspecific taxa support recognition of two new species and recircumscription and placement of elements of the polyphyletic S. ghiesbreghtii and S. mortonii complexes. For taxa with adequate sampling, our data also indicate 11-12 cladospecies and 3-6 metaspecies according to the apomorphic species concept. The resolved phylogeny, correlated with geography and morphology, allows insight into biogeographical diversification and the evolution of some unusual morphological characters within the genus, such as nectary differentiation and tepal margin type.

Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing.

PREMISE OF THE STUDY Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous-particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. METHODS Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses. KEY RESULTS Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades. CONCLUSIONS The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.

Northernmost Limit of Rhizophora mangle (Red Mangrove; Rhizophoraceae) in St. Johns County, Florida

Abstract The northernmost record of Rhizophora mangle (red mangrove), recently vouchered from Fort Matanzas National Monument in St. Johns County, Florida, is discussed in reference to the ecology, morphology, and preservation of the species.

Vascular plant survey of Cumberland Island National Seashore, Camden County, Georgia.

Abstract Cumberland Island National Seashore, Camden County, Georgia, is administered by the National Park Service, United States Department of the Interior, and comprises 14,740 ha (36,415 acres) that include property and historic residences once owned by the Thomas Carnegie family. A floristic survey of the 7,880 ha (19,472 acres) owned by the National Park Service was conducted to provide Park Service personnel with a vouchered plant species checklist, supplemented with salient information such as relative abundance, locality data, and general community type. Six intensive collecting trips conducted in 2004–2006 yielded 498 species of plants, including 233 species not previously vouchered for the Island. The four largest families were Poaceae, Cyperaceae, Asteraceae, and Fabaceae. Identifications of specimens in the Cumberland Island National Museum Herbarium were also verified and incorporated into the annotated list. Maps, descriptions, and photographs of the various plant communities are provided.