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Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, but for many groups of flowering plants fossil evidence is unavailable or limited. Arabidopsis thaliana, the primary genetic model in plant biology and the first plant to have its entire genome sequenced, belongs to one such group, the plant family Brassicaceae. Thus, the timing of A. thaliana evolution and the history of its genome have been controversial. We bring previously overlooked fossil evidence to bear on these questions and find the split between A. thaliana and Arabidopsis lyrata occurred about 13 Mya, and that the split between Arabidopsis and the Brassica complex (broccoli, cabbage, canola) occurred about 43 Mya. These estimates, which are two-to threefold older than previous estimates, indicate that gene, genomic, and developmental evolution occurred much more slowly than previously hypothesized and that Arabidopsis evolved during a period of warming rather than of cooling. We detected a 2-to 10-fold shift in species diversification rates on the branch uniting Brassicaceae with its sister families. The timing of this shift suggests a possible impact of the Cretaceous-Paleogene mass extinction on their radiation and that Brassicales codiversified with pierid butterflies that specialize on mustard-oil-producing plants.he most important genetic model in plant biology is Arabidopsis thaliana. It is the first plant to have its entire genome sequenced, and it serves as a key comparison point with other eukaryotic genomes. A. thaliana is diploid and has a small genome distributed on just five chromosomes, considerations in its choice as a model (1). The age of the Arabidopsis crown group (CG), previously estimated at 5.8-3 Mya (2, 3), and of splits within Brassicaceae have been used to understand the pace of evolution in genes affecting self-incompatibility (4, 5), the rate of change in signal transduction and gene expression (6, 7), the persistence of shared chromosomal rearrangements in A. thaliana and Brassica oleracea (8), the tempo of evolution of miRNA sequences (9), the evolution of pierid butterflies specializing in plants that produce mustard oils (10), and the ages of wholegenome duplication (WGD) events giving rise to gene pairs in Arabidopsis (11). As genomes of additional Brassicaceae (e.g., Capsella rubella) and other Brassicales (e.g., Carica papaya) (12) are sequenced, the importance of robust estimates of divergence dates relating these genomes to one another and to the geological record increases substantially.The accuracy of divergence times inferred from sequence data depends on valid, verifiable fossils to calibrate phylogenetic trees. Previous dates for the origin of Arabidopsis relied on the report of fossil pollen assigned to the genus Rori...

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of <15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107-83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns. community assembly ͉ divergence time estimates ͉ phylogeny ͉ rapid radiation G reat progress has been made in elucidating deep-level angiosperm relationships during the past decade. The eudicot clade, with Ϸ75% of all angiosperm species, comprises several major subclades: rosids, asterids, Saxifragales, Santalales, and Caryophyllales (1-3). Investigations have converged on the branching pattern of the basalmost angiosperms, revealing that Amborellaceae, Nymphaeales [in the sense of APG II (3) and including Hydatellaceae (4)], and Austrobaileyales are successive sisters to all other extant angiosperms (reviewed in ref.2). Analyses of complete plastid genome sequences have resolved other problematic deep-level relationships, suggesting that Chloranthaceae and magnoliids are sister to a clade of monocots and eudicots plus Ceratophyllaceae (5, 6). Likewise, progress has been made in clarifying relationships within the large monocot (7) and asterid (8) clades.Despite these successes, the rosids stand out as the largest and least-resolved major clade of angiosperms; basal nodes within the clade have consistently received low internal support (1, 2, 9, 10). The rosid clade comprises Ϸ70,000 species and 140 families (2, 11). Containing more than a quarter of total angiosperm and Ϸ39% of eudicot species diversity, the rosid clade is broader in circumscription than the traditional Rosidae or Rosanae (e.g., 12; reviewed in ref.2). The oldest fossil flowers conforming to the rosids are from the late S...

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We review the fossil history of seed plant genera that are now endemic to eastern Asia. Although the majority of eastern Asian endemic genera have no known fossil record at all, 54 genera, or about 9%, are reliably known from the fossil record. Most of these are woody (with two exceptions), and most are today either broadly East Asian, or more specifically confined to Sino-Japanese subcategory rather than being endemic to the SinoHimalayan area. Of the "eastern Asian endemic" genera so far known from the fossil record, the majority formerly occurred in Europe and/or North America, indicating that eastern Asia served as a late Tertiary or Quaternary refugium for taxa. Hence, many of these genera may have originated in other parts of the Northern Hemisphere and expanded their ranges across continents and former sea barriers when tectonic and climatic conditions allowed, leading to their arrival in eastern Asia. Although clear evidence for paleoendemism is provided by the gymnosperms Amentotaxus, Cathaya, Cephalotaxus, Cunninghamia, Cryptomeria, Glyptostrobus, Ginkgo, Keteleeria, Metasequoia, Nothotsuga, Pseudolarix, Sciadopitys, and Taiwania, and the angiosperms Cercidiphyllum, Choerospondias, Corylopsis, Craigia, Cyclocarya, Davidia, Dipelta, Decaisnea, Diplopanax, Dipteronia, Emmenopterys, Eucommia, Euscaphis, Hemiptelea, Hovenia, Koelreuteria, Paulownia, Phellodendron, Platycarya, Pteroceltis, Rehderodendron, Sargentodoxa, Schizophragma, Sinomenium, Tapiscia, Tetracentron, Toricellia, Trapella, and Trochodendron, we cannot rule out the possibility that neoendemism plays an important role especially for herbaceous taxa in the present-day flora of Asia, particularly in the Sino-Himalayan region. In addition to reviewing paleobotanical occurrences from the literature, we document newly recognized fossil occurrences that expand the geographic and stratigraphic ranges previously known for Dipelta, Pteroceltis, and Toricellia.

DNA sequences were generated for matK and ITS for 68 and 103 samples of Cornus to reconstruct a species level phylogeny of the genus. The results support the monophyly of most subgenera, except subg. Kraniopsis and subg. Cornus. Subgenus Kraniopsis was suggested to exclude C. peruviana from South America and subg. Afrocrania and subg. Sinocornus were nested within subg. Cornus. Four major clades corresponding to groups also recognizable by morphological differences were revealed: the big‐bracted dogwoods (BB) including subg. Cynoxylon, subg. Syncarpea, and subg. Discocrania, the dwarf dogwoods (DW) including subg. Arctocrania, the cornelian cherries (CC) including subg. Cornus, subg. Sinocornus, and subg. Afrocrania, and the blue‐ or white‐fruited dogwoods (BW) including subg. Kraniopsis, subg. Mesomora, and subg. Yinquania. This finding is consistent with previous studies with more limited sampling. The single South American species C. peruviana was found to be sister to the Asian C. oblonga of subg. Yinquania, adding a fourth intercontinental disjunction in the genus that was previously unknown. Species relationships within the subgenera were clearly resolved except for the relatively large subg. Syncarpea and subg. Kraniopsis. Phylogenetic analyses of total evidence combining morphology, matK, ITS, and previously published rbcL and 26S rDNA sequences resolved the relationships among subgenera as (BW(CC(BB, DW))). Biogeographic analyses using DIVA with or without fossils resulted in different inferences of biogeographic history of the genus, indicating the importance of fossil data in biogeographic analyses. The phylogeny based on the total evidence tree including fossils supports an origin and early Tertiary diversification of Cornus in Europe and multiple trans‐Atlantic migrations between Europe and North America by the early Tertiary. It also supports that distribution of the few species in the southern hemisphere was not ancestral, but a result of migration from the north. This evidence rejects a previous hypothesis of a southern hemispheric origin of the genus.

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