RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae).

Trichophoreae is a nearly cosmopolitan Cyperaceae tribe that contains ~17 species displaying striking variation in size, inflorescence complexity, and perianth morphology. Although morphologically distinct, the status of its three genera (Cypringlea, Oreobolopsis and Trichophorum) is controversial because recent phylogenetic studies have suggested they might not be reciprocally monophyletic. However, previous analyses have shown conflicting topologies and consistently poor support due to an initial rapid diversification of the tribe. We analysed restriction-site associated DNA sequencing (RADseq) data from nearly all species of the clade, combined with five Sanger-based markers (matK, ndhF, rps16, ETS-1f, ITS) sampled extensively within species. This approach allowed us to resolve deep and shallow relationships within Trichophoreae for the first time, despite an anomaly zone spanning several successive short branches that produced considerable gene tree incongruence. Analyses reveal a primary phylogenetic split of the tribe into two clades roughly corresponding to an East Asian-North American disjunction that dates back to the mid-Miocene, with both clades comprised of a mixture of reduced unispicate and larger taxa with highly compound inflorescences. Morphological characters traditionally used in the circumscription of Trichophoreae genera are shown to be homoplasious. Several of these characters correlate best with climatic conditions, with the most reduced species occurring in open habitats at high latitudes and altitudes. Close relatives with highly compound inflorescences are found in temperate or subtropical forest understories. Cypringlea and Oreobolopsis are deeply nested within Trichophorum, and we merge all three genera into a more broadly circumscribed Trichophorum. We also show that Scirpus filipes is another previously unrecognized East Asian species of Trichophorum with highly compound inflorescences.

The rediscovery of the rare Vietnamese endemic Eriophorum scabriculme redefines generic limits in the Scirpo-Caricoid Clade (Cyperaceae).

For those familiar with boreal bogs and wet tundra, species of Eriophorum ("the cotton grasses") will undoubtedly represent some of the most striking and memorable taxa they have encountered. This small genus of 20 Holarctic sedge species (Cyperaceae) is remarkable because its inflorescences produce large, brilliantly white to rusty-red cottony masses when its flowers develop a perianth of highly elongated bristles after anthesis. In this study, we document the rediscovery of Eriophorum scabriculme, a narrow Vietnamese endemic known from only two collections made approximately 7 km apart near Sa Pa in Lào Cai Province over 75 years ago. Using plastid DNA sequences (matK, ndhF), embryology, and morphology, we test whether E. scabriculme is aligned within the Scirpo-Caricoid Clade (genus Khaosokia and tribes Cariceae, Dulichieae, Scirpeae, and Sumatroscirpeae) or the Ficinia Clade (Cypereae), and we determine whether its unique character combinations (≥10 elongated bristles, reduced sheathing basal leaves, 1-4 spikelets) could be evidence for a new genus or simply mark it as an unusual species within currently recognised genera. In addition, we document the discovery of seven new populations, and we extend its range westward to Lai Châu Province and southward in Lào Cai Province by more than 47 km. Our results demonstrate that Eriophorum scabriculme is best treated in the genus Trichophorum, thus re-circumscribing both genera and their limits with Scirpus s.str. In addition, we emend the description of Trichophorum scabriculme (Beetle) J.R.Starr, Lév.-Bourret & B.A. Ford, provide the first pictures and accurate illustration of the species, and assess its conservation status in Vietnam (VU, Vulnerable). Our study corroborates the fact that in such a diverse and taxonomically difficult family like the sedges, conspicuous characters like highly elongated bristles may be useful for dividing diversity, but they are no guarantee that the groups they mark are natural.

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics.

Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high-copy numbers and universal polymerase chain reaction (PCR) primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant-specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: Weak or unresolved backbone due to rapid radiations ($\leqslant $10 million years) followed by long divergence, using the Cariceae-Dulichieae-Scirpeae (CDS, Cyperaceae) clade as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger-sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both concatenated and coalescence-based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long-branch attraction. The robust phylogenetic estimates obtained here, and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS clade. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups.

Why are there so many sedges? Sumatroscirpeae, a missing piece in the evolutionary puzzle of the giant genus Carex (Cyperaceae).

For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers. Ancestral state reconstructions of key characters were made, and a time-calibrated tree estimated. Carex is strongly supported as sister to the rare East Asian Sumatroscirpus, sole genus of a new tribe, Sumatroscirpeae trib. nov. Believed to be unique to Carex, the perigynium (prophyllar bract enclosing a flower) is in fact a synapomorphy shared with this small tribe (∼4 species) that appeared 36 Mya. We thus suggest the initial key innovation in the remarkable diversification of Carex is not the perigynium, but could be the release of mechanical constraints on perigynia through spikelet truncation, resulting in novel adaptive morphologies. Monoecy, chromosomal change, and rapid inflorescence development enabling phenological isolation may also be involved. The tiny tribe Sumatroscirpeae will provide unprecedented insights into the inflorescence homology, evolution, diversification, and biogeographic history of its sister-group Carex, one of the world's most diverse plant lineages.

Three new, early diverging Carex (Cariceae, Cyperaceae) lineages from East and Southeast Asia with important evolutionary and biogeographic implications.

Traditional Cariceae and Carex (1966 spp.) classifications recognised five genera (Carex, Cymophyllus, Kobresia, Schoenoxiphium, Uncinia) and four subgenera (Carex, Vignea, Vigneastra, Psyllophora). However, molecular studies have shown that only Carex, divided into five major lineages (the Core Carex, Schoenoxiphium, Core Unispicate, Vignea and Siderostictae Clades), is natural. These studies have also suggested that many early diverging tribal lineages are East Asian in origin, but the sampling of East Asian groups has been poor, and support for relationships within and among major Cariceae clades has been weak. To test deep patterns of relationship in Carex we assembled the longest sequence dataset yet (ITS, ETS 1f, matK, ndhF, rps16; ca. 4400bp) with taxonomic sampling focused on critical East and Southeast Asian Carex sections that have blurred subgeneric limits (Decorae, Graciles, Mundae) or have been at the heart of theories on tribal origins (Hemiscaposae, Indicae, Surculosae, Euprepes, Mapaniifoliae, Hypolytroides). Results indicate that subg. Vigneastra is highly polyphyletic (in five of seven major lineages recognised), and they provide the strongest support yet seen for all previously recognised major Cariceae clades in a single analysis (⩾93% BS). Moreover, results provide strong evidence for three previously unrecognised early diverging East and Southeast Asian lineages: a "Hypolytroides Clade" (sect. Hypolytroides) sister to the Siderostictae Clade, and for a "Dissitiflora Lineage" (sect. Mundae) and a morphologically diverse "Small Core Carex Clade" (sects. Graciles, Decorae, Mapaniifoliae, Euprepes, Indicae) as successive sisters to approximately 1400 species in the Core Carex Clade. Our findings also suggest that morphological diversification may have occurred in clades dominated by Asian species followed by canalization to a narrower range of morphologies in species-rich, cosmopolitan lineages.

Comparative population structure and genetic diversity of Arceuthobium americanum (Viscaceae) and its Pinus host species: insight into host-parasite evolution in parasitic angiosperms.

In a recent study we revealed that the parasitic angiosperm Arceuthobium americanum is comprised of three distinct genetic races, each associated with a different host in regions of allopatry. In order to assess the role of host identity and geographical isolation on race formation in A. americanum, we compared the genetic population structure of this parasite with that of its three principal hosts, Pinus banksiana, Pinus contorta var. latifolia and Pinus contorta var. murrayana. Despite the fact that A. americanum was divided into three genetic races, hosts were divided into only two genetic groups: (i) Pinus banksiana and hybrids, and (ii) P. contorta var. latifolia and var. murrayana. These findings suggest that factors such as geographical isolation and adaptation to different environmental conditions are important for race formation in the absence of host-driven selection pressures. To assess factors impacting population structure at the fine-scale, genetic and geographical distance matrices of host and parasite were compared within A. americanum races. The lack of a relationship between genetic and geographical distance matrices suggests that isolation-by-distance plays a negligible role at this level. The effect of geographical isolation may have been diminished because of the influence of factors such as random seed dispersal by animal vectors or adaptation to nongeographically patterned environmental conditions. Host-parasite interactions might also have impacted the fine-scale structure of A. americanum because the parasite and host were found to have similar patterns of gene flow.

The discovery of three genetic races of the dwarf mistletoe Arceuthobium americanum (Viscaceae) provides insight into the evolution of parasitic angiosperms.

A population genetic approach was used to explore the evolutionary biology of the parasitic angiosperm Arceuthobium americanum Nutt. ex Engelm. (Viscaceae). Arceuthobium americanum infects three principal hosts and has the most extensive geographical range of any North American dwarf mistletoe. Based on the lack of apparent morphological and phenological differences between populations of A. americanum, past researchers have found no evidence for recognizing infraspecific taxa. In this study, molecular analysis using amplified fragment length polymorphism (AFLP) analysis indicated that A. americanum is divided into three distinct genetic races, each associated with a different host taxon in regions of allopatry: (i) Pinus banksiana in western Canada; (ii) Pinus contorta var. murrayana in the Sierra Nevada and Cascade Mountain ranges in the western US; and (iii) Pinus contorta var. latifolia in the western US and Canada. These observations suggest that host identity, geographical isolation and environmental factors have contributed to race formation in A. americanum. The lack of fine-scale patterning within each of the A. americanum races is attributed to random dispersal of seeds over long distances by animal vectors. Historical factors such as glaciations and founder events have also influenced structuring and genetic diversity in A. americanum populations. Given sufficient time, it is possible that these races will become reproductively isolated and undergo speciation.