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.

Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.

be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations.

Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para-or polyphyletic. Yet, taxonomists continue to use subgenera and sections in Carex classification. Why? The Global Carex Group (GCG) here takes the position that the historical and continued use of subgenera and sections serves to (i) organize our understanding of lineages in Carex, (ii) create an identification mechanism to break the~2000 species of Carex into manageable groups and stimulate its study, and (iii) provide a

The field of systematics is experiencing a new molecular revolution driven by the increased availability of high-throughput sequencing technologies. As these techniques become more affordable, the increased genomic resources have increasingly far-reaching implications for our understanding of the Tree of Life. With c. 2000 species, Carex (Cyperaceae) is one of the five largest genera of angiosperms and one of the two largest among monocots, but the phylogenetic relationships between the main lineages are still poorly understood. We designed a Cyperaceae-specific HybSeq bait kit using transcriptomic data of Carex siderosticta and Cyperus papyrus. We identified 554 low-copy nuclear orthologous loci, targeting a total length of c. 1 Mbp. Our Cyperaceae-specific kit shared loci with a recently published angiosperm-specific Anchored Hybrid Enrichment kit, which enabled us to include and compile data from different sources. We used our Cyperaceae kit to sequence 88 Carex spp., including samples of all the five major clades in the genus. For the first time, we present a phylogenetic tree of Carex based on hundreds of loci (308 nuclear exon matrices, 543 nuclear intron matrices and 66 plastid exon matrices), demonstrating that there are six strongly supported main lineages in Carex: the Siderostictae, Schoenoxiphium, Unispicate, Uncinia, Vignea and Core Carex clades. Based on our results, we suggest a revised subgeneric treatment and provide lists of the species belonging to each of the subgenera. Our results will inform future biogeographic, taxonomic, molecular dating and evolutionary studies in Carex and provide the step towards a revised classification that seems likely to stand the test of time.

Plants with a native (i.e., naturally occurring or nonanthropogenic) American amphitropical disjunct (AAD) distribution, occurring on both sides of, but not within, the American tropics, have long been recognized as a repeating biogeographic pattern found in a number of plant groups (

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AimThe bipolar disjunction, a biogeographical pattern defined by taxa with a distribution at very high latitudes in both hemispheres (> 61° N; > 54° S), is only known to occur in about 30 vascular plant species. Our aim was to use the bipolar species Carex arctogena to test the four classic hypotheses proposed to explain this exceptional disjunction: convergent evolution, vicariance, mountain--hopping and direct long--distance dispersal.Location Arctic/boreal and temperate latitudes of both hemispheres.Methods A combination of molecular and bioclimatic data was used to test phylogeographical hypotheses in C. arctogena. Three chloroplast markers (atpF-atpH, matK and rps16) and the nuclear ITS region were sequenced for all species in Carex sections Capituligerae and Longespicatae; Carex rupestris, C. obtusata and Uncinia triquetra were used as outrgroups. Phylogenetic relationships, divergence--time estimates and biogeographical patterns were inferred using maximum likelihood, statistical parsimony and Bayesian inference.Results Carex sections Capituligerae and Longespicatae formed a monophyletic group that diverged during the late Miocene. Two main lineages of C. arctogena were inferred.Southern Hemisphere populations of C. arctogena shared the same haplotype as a widespread circumboreal lineage. Bioclimatic data shows that Southern and NorthernHemisphere populations currently differ in their ecological regimes. Main conclusionsTwo of the four hypotheses accounting for bipolar disjunctions may be rejected. Our results suggest that direct long--distance dispersal, probably southwards and mediated by birds, best explains the bipolar distribution of C. arctogena.