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Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for ‘deep’ relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.

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.

We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.

Background and AimsZingiberales 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.MethodsNext-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 ResultsCodon-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.ConclusionsMany 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.

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).

The South Atlantic Coastal Plain Limestone Forest is a globally imperiled (G2) association restricted to the upper Coastal Plain of central Georgia. We conducted a comprehensive floristic inventory of this unique forest type during 2008–2011 at 7 sites (total of 44.67 ha [110.60 ac]) in Houston, Bleckley and Twiggs counties. The survey documented 336 vascular plant species in 98 families. The largest families were Asteraceae (28 spp.), Cyperaceae (22 spp.), Poaceae (19 spp.), Fabaceae (17 spp.), Rosaceae (16 spp.), and Fagaceae (14 spp.). Only 4.2% of this flora was non-native. Seventeen species were listed as rare, including the federally endangered Silene catesbaei. We provide a vouchered plant checklist for this association and general descriptions of the 3 main vegetation communities: uplands, slopes, and bottomlands.

• 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.

Veratrum woodii, a long-lived herbaceous perennial species, has a fragmented distribution with populations scattered in the southeastern and lower midwestern USA. In Georgia, the species has a protection status of rare. This preliminary study focused on verifying historic and/or unvouchered populations in Georgia and characterizing variation and genetic structure within and among all populations in the state. We analyzed AFLP (amplified fragment length polymorphism) data as dominantly inherited markers for 16 populations sampled from Georgia, Florida, and Missouri. Our results suggest that this species overall has relatively low levels of genetic diversity and that differentiation among populations is comparable to species with similar life history traits. Measures of genetic diversity, such as mean He, indicate that variation of populations has some partitioning between disjunct northern and southern Georgia (and Florida) populations. However, our analyses imply that watershed assignment, rather than geographic distance, provides a better explanation for variation and population structure. We hypothesize that southern relict populations in Georgia may have served as refugia during Pleistocene glaciations. We conclude that life-history characteristics, low levels of genetic variation, and suppression of ecological disturbance collectively jeopardize populations of Veratrum woodii in Georgia.

The monotypic genus Zigadenus occupies a critical position in the evolution of Melanthieae as sister to the clade comprising the rest of the genera in the tribe. Meiotic (n = 27) and mitotic (2n = 54) chromosome counts for Zigadenus glaberrimus documented here do not support a long-standing tentative report of 2n = 52. The likely base chromosome number of the tribe and significance of chromosome numbers as generic synapomorphies are discussed in reference to these newly recorded counts for Zigadenus glaberrimus, a likely hexaploid.

Stone Mountain in DeKalb County, Georgia, is a large exposed granite monolith, 514 m (1,686 ft) above sea level and covering 230 ha (560 ac). This monadnock is located in the southwestern portion of Stone Mountain Park, comprising 1,300 ha (3,212 ac) owned by the state of Georgia. Recent specimen digitization efforts at the University of Georgia Herbarium (GA) have greatly facilitated capture of data from historic vouchers collected from this park. Based on these newly available data, the goals of this project were to (1) prepare a vouchered species list for the park, (2) produce a vegetation map based on georeferenced label data, and (3) identify all plant collectors and track collection activities through time and taxon focus. Eighty-one individuals and teams collected 1,207 vouchers (709 species) dated 1846–2011. The largest families were Asteraceae (96 spp.), Poaceae (70 spp.), Fabaceae (49 spp.), Cyperaceae (33 spp.), Rosaceae (21 spp.), and Lamiaceae (20 spp.). Approximately 17.5% of the species were exotic. Eighteen species are listed as rare in Georgia with state protection status conferred on five species; Gratiola amphiantha (threatened) and Isoetes melanospora (endangered) are also federally ranked. Specimen label data and various map resources were used to plot the locality of each specimen. Habitat data were recorded on 808 specimen labels, allowing assignment of 612 taxa to at least one of five general habitat types. GPS coordinates, assigned through GeoLocate, were combined with habitat data and infrared imagery to create a general vegetation map of Stone Mountain Park.