The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a “museum” of extant species diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space.

Asteraceae are the largest family of dicotyledonous plants and have long been known for their taxonomie complexity. The ubiquitous parallelisms in morphology within the family have made phylogenetic reconstruction and tribal circumscription an area of long debate. In this study we explored the utility of using two relatively short non-coding chloroplast DNA sequences, the trnL intron and IrnUtrnV intergenic spacer, to resolve phylogenetic relationships among the tribes. The results of the phylogenetic analysis produced trees that are topologically congruent with prior phylogenetic hypotheses based on both morphological and molecular data sets. The Asteroideae are a monophyletic group, but the Cichorioideae are paraphyletic. The primary clades of the Cichorioideae are the Mutisieae-Cardueae, Liabeae-Vernonieae, and of the Asteroideae, the Inuleae-Plucheeae, Astereae-Anthemideae, Senecioneae-Gnaphalieae, and the helianthoid clade (Helenieae, Heliantheae s.str.. and Eupatorieae). The Inuleae-Plucheeae clade is sister to the remainder of the Asteroideae. and the paraphyly of the Inuleae 8.1. (Gnaphalieae. Inuleae s. str., and Plucheeae) is firmly supported by our analysis. Our study illustrates the utility of the trnL intron and trnUV intergenic spacer for resolving relationships among tribes of the Asteraceae. Using approximately 874 bp, we were able to produce a phylogeny of comparable resolution to phylogenies based on well-known coding regions such as rbc\, and ndhY. For phylogenetic inference at the family level the trnL intron and trnUV spacer provide similar levels of resolution to longer coding sequences (e.g.. rbcL, ndhF), while having the advantage of being much easier to amplify and sequence due to their short lengths and universal primers. The numerous insertions and deletions commonly found in this region are easily aligned and are phylogenetically informative, thus adding considerably to the information content per base pair sequenced.

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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 bestknown 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., ³ 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.