Robert F. C. Naczi

Phylogeny of Cyperaceae Based on DNA Sequence Data: Current Progress and Future Prospects

In the last decade, efforts to reconstruct suprageneric phylogeny of the Cyperaceae have intensified. We present an analysis of 262 taxa representing 93 genera in 15 tribes, sequenced for the plastid rbcL and trnL-F (intron and intergenic spacer). Cyperaceae are monophyletic and resolved into two clades, here recognised as Mapanioideae and Cyperoideae, and the overall topology is similar to results from previous studies. Within Cyperoideae, Trilepideae are sister to rest of taxa whereas Cryptangieae, Bisboeckelerieae and Sclerieae are resolved within Schoeneae. Cladium and Rhynchospora (and Pleurostachys) are resolved into clades sister to the rest of Schoeneae, lending support to the recognition of these taxa in separate tribes. However, we retain these taxa in Schoeneae pending broader sampling of the group. The phylogenetic position of 40 species in 21 genera is presented in this study for the first time, elucidating their position in Abildgaardieae (Trachystylis), Cryptangieae (Didymiandrum, Exochogyne), Cypereae (Androtrichum, Volkiella), Eleocharideae (Chillania), and Schoeneae (Calyptrocarya, Morelotia). More sampling effort (more taxa and the use of more rapidly evolving markers) is needed to resolve relationships in Fuireneae and Schoeneae.

Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae).

We investigate the species discriminatory power of a subset of the proposed plant barcoding loci (matK, rbcL, rpoC1, rpoB, trnH‐psbA) in Carex, a cosmopolitan genus that represents one of the three largest plant genera on earth (c. 2000 species). To assess the ability of barcoding loci to resolve Carex species, we focused our sampling on three of the taxonomically best‐known groups in the genus, sections Deweyanae (6/8 species sampled), Griseae (18/21 species sampled), and Phyllostachyae (10/10 species sampled). Each group represents one of three major phylogenetic lineages previously identified in Carex and its tribe Cariceae, thus permitting us to evaluate the potential of DNA barcodes to broadly identify species across the tribe and to differentiate closely related sister species. Unlike some previous studies that have suggested that plant barcoding could achieve species identification rates around 90%, our results suggest that no single locus or multilocus barcode examined will resolve much greater than 60% of Carex species. In fact, no multilocus combination can significantly increase the resolution and statistical support (i.e., ≥ 70% bootstrap) for species than matK alone, even combinations involving the second most variable region, trnH‐psbA. Results suggest that a matK barcode could help with species discovery as 47% of Carex taxa recently named or resolved within cryptic complexes in the past 25 years also formed unique species clusters in upgma trees. Comparisons between the nrDNA internal transcribed spacer region (ITS) and matK in sect. Phyllostachyae suggest that matK not only discriminates more species (50–60% vs. 25%), but it provides more resolved phylogenies than ITS. Given the low levels of species resolution in rpoC1 and rpoB (0–13%), and difficulties with polymerase chain reaction amplification and DNA sequencing in rbcL and trnH‐psbA (alignment included), we strongly advocate that matK should be part of a universal plant barcoding system. Although identification rates in this study are low, they can be significantly improved by a regional approach to barcoding.

Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this familys phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44–53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25–44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14–32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2–7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya. Overall, these results suggest climatic change at different temporal and spatial scales in part shaped the distribution and diversity of this carnivorous plant clade.

Megaphylogenetic Specimen-Level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for Classification

Abstract We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, historical misunderstanding of how morphology varies across Carex, and regional rather than global views of Carex diversity seem to be the main reasons for the high levels of polyphyly and paraphyly in the current infrageneric classification.

Insights on Using Morphologic Data for Phylogenetic Analysis in Sedges (Cyperaceae)

Sedges are often viewed as difficult subjects for morphology-based phylogenetic analysis, due to several difficulties, including finding an adequate number of characters to yield well-resolved and well-supported trees, correctly assessing homology of characters and character states, and selecting appropriate outgroups for character state polarizations. The published literature holds only 11 papers with morphology-based phylogenetic analyses of sedges. This paper reviews those studies, and presents the phylogeny of two groups of sedges: (1) Carex section Deweyanae, and (2) Carex sections Careyanae, Granulares, and Griseae. This paper also presents recommendations for using morphologic data to reconstruct sedge phylogenies, based on comparisons of the trees resulting from the present study with the previous sedge studies and with similar studies of phylogeny of other groups of flowering plants. In the two groups of Carex examined, morphology does provide sufficient characters to infer well-resolved trees, with some nodes having good to strong support at levels consistent with those found in morphology-based analyses of other groups of flowering plants. The inclusion of micromorphologic and anatomic characters substantially enhances the resolving power of macromorphologic characters in sedge analyses, and increases the support for some clades.

Pitcher Plants (Sarracenia) Provide a 21st-Century Perspective on Infraspecific Ranks and Interspecific Hybrids: A Modest Proposal* for Appropriate Recognition and Usage

Abstract The taxonomic use of infraspecific ranks (subspecies, variety, subvariety, form, and subform), and the formal recognition of interspecific hybrid taxa, is permitted by the International Code of Nomenclature for algae, fungi, and plants. However, considerable confusion regarding the biological and systematic merits is caused by current practice in the use of infraspecific ranks, which obscures the meaningful variability on which natural selection operates, and by the formal recognition of those interspecific hybrids that lack the potential for inter-lineage gene flow. These issues also may have pragmatic and legal consequences, especially regarding the legal delimitation and management of threatened and endangered species. A detailed comparison of three contemporary floras highlights the degree to which infraspecific and interspecific variation are treated inconsistently. An in-depth analysis of taxonomy of the North American flowering plant genus Sarracenia (Sarraceniaceae) provides an ideal case study illustrating the confusion that can arise from inconsistent and apparently arbitrary designation of infraspecific ranks and hybrid taxa. To alleviate these problems, we propose the abandonment of infraspecific ranks of “variety” and “form,” and discourage naming of sterile interspecific hybrids except for use in the horticultural or agronomic trade. Our recommendations for taxonomic practice are in accord with the objectives proposed in the Systematics Agenda 2000, Systematics Agenda 2020, and the Global Strategy for Plant Conservation.

Calliscirpus, a new genus for two narrow endemics of the California Floristic Province, C. criniger and C. brachythrix sp. nov. (Cyperaceae)

SummaryAlthough the polyphyletic genus Scirpus L. s.l. (formerly > 200 species) has been divided into more than 50 separate genera and now consists of only 64 species, its circumscription remains problematical. Three new genera have been segregated from Scirpus s.s. in the past decade, and the delimitation of Scirpus from its possible sister genus Eriophorum L. (c. 18 species) is still unresolved. The primary character used to delimit Eriophorum from Scirpus is ≥ 10 smooth, elongate perianth bristles vs ≤ 6 short, serrulate bristles or a lack of bristles, but some species display character combinations that make it difficult to place them in either genus. Eriophorum crinigerum (A. Gray) Beetle (= Scirpus criniger A. Gray), endemic to the California Floristic Province, USA, is one such species, possessing a unique combination of bristle and inflorescence features that suggest affinities with both Scirpus and Eriophorum. In this study we use molecular (matK, ndhF), morphological, and embryological data to demonstrate that E. crinigerum is not closely related to either Scirpus or Eriophorum, but represents a new generic lineage, here named Calliscirpus C. N. Gilmour, J. R. Starr & Naczi (tribe Scirpeae). Within the genus, molecular (matK, ETS 1f) and morphological data strongly support the recognition of two species, each of which is restricted to a distinct region of high endemism. Calliscirpus criniger (A. Gray) C. N. Gilmour, J. R. Starr & Naczi comb. nov. is common to the Klamath-Siskiyou and North Coast mountain ranges of Oregon and California, whereas a new species, Calliscirpus brachythrix C. N. Gilmour, J. R. Starr & Naczi, is unique to the Sierra Nevada mountain range of California. Scirpus maximowiczii C. B. Clarke, another transitional species that has blurred the limits of Scirpus and Eriophorum, and has been cited as morphologically similar to Calliscirpus species in the past, is strongly placed within a Scirpus s.s. + Eriophorum s.s. clade (100% bootstrap) on the basis of molecular and embryological data. Tree support and taxonomic sampling are not sufficient to resolve the delimitation of Eriophorum s.s. from Scirpus s.s.

Carex secalina (Cyperaceae), an Introduced Sedge New to North America

Abstract Carex secalina, a species native to eastern Europe and Asia, is reported as a new naturalized member of the North America flora. There are currently seven known populations in North America, all in southeastern New York State. In its native range, it is a species of damp or wet, often saline soils. In North America, it is known to grow predominately in highly disturbed urban habitats, including areas influenced by salt. It currently does not appear to be invasive in North America, but further monitoring is warranted due to its high potential fecundity. The updated Köppen-Geiger climate classification model is used to assess potential regions in North America where C. secalina might grow. Carex secalina is easily distinguished from all other members of the North American flora by a combination of the perigynia being very sharply two-angled and the spikes being pedunculate, especially proximally. Images of the species and its habitat in North America are presented, as are maps showing its distribution in its native and introduced ranges.

Taxonomy, Morphology, and Geographic Distribution of Juncus Longii (Juncaceae)

Abstract Authors have debated the taxonomic status of Juncus longii almost since its description in 1937. Some authors treat the J. marginatus complex, to which J. longii belongs, as comprised of three species (J. biflorus, J. longii and, J. marginatus), whereas other authors recognize only one species (J. marginatus). Univariate and multivariate statistical analyses of measurements of twelve morphological characters suggest that Juncus longii is a species distinct from J. marginatus and J. biflorus. Ecological differences are also apparent. Juncus longii is restricted to early successional seepages with exposed soils. Juncus marginatus and J. biflorus, however, are found in less specialized habitats. Syntopic occurrences of J. longii with J. marginatus and J. longii with J. biflorus suggest the morphological differences used to identify these species are not a reflection of environmental conditions. Juncus longii is endemic to the southeastern United States, whereas J. biflorus and J. marginatus are more broadly distributed across eastern North America, Central America and central South America.

Revision of the Rhynchospora glomerata species complex, focusing on the taxonomic status of R. leptocarpa (Cyperaceae)

Rhynchospora glomerata and its closest relatives comprise a group of beakesedges widespread and frequent in much of North America. The classification of the R. glomerata complex remains unresolved and controversial. The goals of this study are to determine the number of taxa in the complex and their ranks, and identify their best diagnostic characters. Measurements of eight characters from each of 101 specimens from throughout the geographic range of the complex furnished data for morphometric analyses. These analyses reveal the R. glomerata complex contains three species and no infraspecific taxa: R. capitellata, R. glomerata, and R. leptocarpa. We detected 10 validly published basionyms in the complex, five of which required lectotypification. Accordingly, we designated lectotypes for R. glomeratavar.discutiens, R. glomeratavar.minor, R. glomeratavar.paniculata, and R. glomeratavar.robustior, and the second-step lectotype for R. capitellatavar.controversa.