Phylogenetic relationships of Carpha and its relatives (Schoeneae, Cyperaceae) inferred from chloroplast trnL intron and trnL–trnF intergenic spacer sequences

Revision of the Afro-Madagascan genus Costularia (Schoeneae, Cyperaceae): infrageneric relationships and species delimitation

A recent molecular phylogenetic study revealed four distinct evolutionary lineages in the genus Costularia s.l. (Schoeneae, Cyperaceae, Poales). Two lineages are part of the Oreobolus clade of tribe Schoeneae: the first being a much-reduced genus Costularia s.s., and the second a lineage endemic to New Caledonia for which a new genus Chamaedendron was erected. The other two lineages were shown to be part of the Tricostularia clade of tribe Schoeneae. Based on morphological and molecular data, the genus Costularia is here redelimited to represent a monophyletic entity including 15 species, which is restricted in distribution to southeastern Africa (Malawi, Mozambique, South Africa, Swaziland, Zimbabwe), Madagascar, the Mascarenes (La Réunion, Mauritius), and the Seychelles (Mahé). Molecular phylogenetic data based on two nuclear markers (ETS, ITS) and a chloroplast marker (trnL-F) resolve the studied taxa as monophyletic where multiple accessions could be included (except for Costularia laxa and Costularia purpurea, which are now considered conspecific), and indicate that the genus dispersed once to Africa, twice to the Mascarenes, and once to the Seychelles. Two endemic species from Madagascar are here described and illustrated as new to science, as is one additional species endemic to La Réunion. Two taxa previously accepted as varieties of Costularia pantopoda are here recognised at species level (Costularia baronii and Costularia robusta). We provide a taxonomic revision including an identification key, species descriptions and illustrations, distribution maps and assessments of conservation status for all species.

Molecular phylogenetics of the genus Costularia (Schoeneae, Cyperaceae) reveals multiple distinct evolutionary lineages

We investigated the monophyly of Costularia (25 species), a genus of tribe Schoeneae (Cyperaceae) that illustrates a remarkable distribution pattern from southeastern Africa, over Madagascar, the Mascarenes and Seychelles, to Malesia and New Caledonia. A further species, Tetraria borneensis, has been suggested to belong to Costularia. Relationships and divergence times were inferred using an existing four marker phylogeny of Cyperaceae tribe Schoeneae expanded with newly generated sequence data mainly for Costularia s.l. species. Phylogenetic reconstruction was executed using Bayesian inference and maximum likelihood approaches. Divergence times were estimated using a relaxed molecular clock model, calibrated with fossil data. Based on our results, Tetraria borneensis is not related to the species of Costularia. Costularia s.l. is composed of four distinct evolutionary lineages. Two lineages, one including the type species, are part of the Oreobolus clade, i.e. a much reduced genus Costularia restricted to southeastern Africa, Madagascar, the Mascarenes and Seychelles, and a small endemic genus from New Caledonia for which a new genus Chamaedendron is erected based on Costularia subgenus Chamaedendron. The other two lineages are part of the Tricostularia clade, i.e. a separate single-species lineage from the Seychelles for which a new genus (Xyroschoenus) is described, and Costularia subgenus Lophoschoenus. For the latter, more research is needed to test whether they are congeneric with the species placed in the reticulate-sheathed Tetraria clade.

Radiation and repeated transoceanic dispersal of Schoeneae (Cyperaceae) through the southern hemisphere

PREMISE OF THE STUDY

The broad austral distribution of Schoeneae is almost certainly a product of long-distance dispersal. Owing to the inadequacies of existing phylogenetic data and a lack of rigorous biogeographic analysis, relationships within the tribe remain poorly resolved and its pattern of radiation and dispersal uncertain. We employed an expanded sampling of taxa and markers and a rigorous analytic approach to address these limitations. We evaluated the roles of geography and ecology in stimulating the initial radiation of the group and its subsequent dispersal across the southern hemisphere.

METHODS

A dated tree was reconstructed using reversible-jump Markov chain Monte Carlo (MCMC) with a polytomy prior and molecular dating, applied to data from two nuclear and three cpDNA regions. Ancestral areas and habitats were inferred using dispersal-extinction-cladogenesis models.

KEY RESULTS

Schoeneae originated in Australia in the Paleocene. The existence of a "hard" polytomy at the base of the clade reflects the rapid divergence of six principal lineages ca. 50 Ma, within Australia. From this ancestral area, Schoeneae have traversed the austral oceans with remarkable frequency, a total of 29 distinct dispersal events being reported here. Dispersal rates between landmasses are not explicable in terms of the geographical distances separating them. Transoceanic dispersal generally involved habitat stasis.

CONCLUSIONS

Although the role of dispersal in explaining global distribution patterns is now widely accepted, the apparent ease with which such dispersal may occur has perhaps been under-appreciated. In Schoeneae, transoceanic dispersal has been remarkably frequent, with ecological opportunity, rather than geography, being most important in dictating dispersal patterns.

Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae)

PREMISE OF THE STUDY

Understanding heterogeneity in species richness across the tree of life is a challenge in evolutionary biology. The sedge family, Cyperaceae, is classified into tribes that exhibit a roughly 200-fold range in species richness. The Cyperaceae present an excellent case study in the determinants of species richness within higher-level taxa.

METHODS

We used secondary calibration based on prior studies and fossils from a rush (Juncaceae) and five sedges to calibrate two previously published Cyperaceae phylogenies, then compared our results to previous molecular clock analyses. We used an information-theoretic approach to identify shifts in lineage diversification rates and phylogenetic generalized least squares to fit alternative models of clade species richness.

KEY RESULTS

Our results suggest a late Cretaceous origin for Cyperaceae (76-89 mya). The inferred 0.06 speciation events Ma(-1) is comparable to overall diversification rates in the order Poales but faster than angiosperm background rates. A threefold increase in diversification rate at the base of the species-rich SDC+FAEC clade is correlated with climatic changes during the Paleocene-Eocene boundary (ca. 55 mya). The greater driver of among-clade variance in species richness, however, is clade age (simple R(2) = 0.334, P = 0.0006).

CONCLUSIONS

Although shifts in diversification rates play a role in the generation of heterogeneous patterns of species richness, our study demonstrates that variance in clade age alone explains ca. 33% of among-clade variation in species diversity, which stands in contrast to the general pattern for angiosperms.

Using supermatrices for phylogenetic inquiry: an example using the sedges

In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic of supermatrix approaches may yield very good estimates of phylogeny. We present a novel pipeline for filtering sparse alignments to improve their phylogenetic utility by maximizing the partial decisiveness of the matrices themselves through a technique we call "phylogenetic scaffolding," and we present a new method of scoring tip instability (i.e. "rogue taxa") based on the I statistic implemented in the software Mesquite. The modified statistic, which we call I(S), is somewhat more straightforward to interpret than similar statistics, and our implementation of it may be applied to large sets of large trees. The largest sedge trees presented here contain more than 1500 tips (about one quarter of all sedge species) and are based on multigene alignments with more than 20 000 sites and more than 90% missing data. These trees match well with previously supported phylogenetic hypotheses, but have lower overall support values and less resolution than more heavily filtered trees. Our best-resolved trees are characterized by stronger support values than any previously published sedge phylogenies, and show some relationships that are incongruous with previous studies. Overall, we show that supermatrix methods offer powerful means of pursuing phylogenetic study and these tools have high potential value for many systematic biologists.

A phylogeny of the schoenoid sedges (Cyperaceae: Schoeneae) based on plastid DNA sequences, with special reference to the genera found in Africa

Despite its large size (about 700 species), the australy-centred sedge tribe Schoeneae has received little explicit phylogenetic study, especially using molecular data. As a result, generic relationships are poorly understood, and even the monophyly of the tribe is open to question. In this study, plastid DNA sequences (rbcL, trnL-trnF, and rps16) drawn from a broad array of Schoeneae are analysed using Bayesian and parsimony-based approaches to infer a framework phylogeny for the tribe. Both analytical methods broadly support the monophyly of Schoeneae, Bayesian methods doing so with good support. Within the schoenoid clade, there is strong support for a series of monophyletic generic groupings whose interrelationships are unclear. These lineages form a large polytomy at the base of Schoeneae that may be indicative of past radiation, probably following the fragmentation of Gondwana. Most of these lineages contain both African and non-African members, suggesting a history of intercontinental dispersal. The results of this study clearly identify the relationships of the African-endemic schoenoid genera and demonstrate that the African-Australasian genus Tetraria, like Costularia, is polyphyletic. This pattern is morphologically consistent and suggests that these genera require realignment.