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A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene., (© 2023 Institute of Botany, Chinese Academy of Sciences.)

The Northern Hemisphere was widely covered by a tropical flora (i.e., the Boretropical flora) in the Eocene and the evaluation of plant diversifications in the post-Boreotropical era has become an important challenge to understanding the modern biogeographic complexity in this vast region. Toxicodendron or the poison ivy genus of the sumac family has a temperate to tropical distribution in Asia and North America and can serve as an excellent model for investigating the evolution of the post-Boreotropical biogeographic complexity. Molecular age estimates were calculated using a Bayesian approach with sampling covering the taxonomic diversity and biogeographic distributions within the genus, and sequence data from three nuclear DNA (ITS, ETS, NIA-i3) and two chloroplast (ndhF, trnL-F) regions, combined with calibrations from three fossil records. Ancestral areas were reconstructed using RASP and BioGeoBears. Toxicodendron is estimated to have a Boreotropical origin in the New World in the late Eocene at 37.68 Ma. It then diversified into a subtropical-temperate and a tropical lineage, followed by migrating into eastern Asia via the North Atlantic land bridges in the Oligocene to early Miocene. Two tropical migration events during the Miocene are identified between continental Asia and SE Asia or New Guinea around 20.91 Ma and 14.33 Ma, respectively. Results from this study highlight the importance of the North Atlantic land bridges and eastern Asia in the post-Boreotopical plant divergences in the Northern Hemisphere, especially when biogeographic exchanges between North and South America were limited., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Linnaeoideae is a small subfamily of erect or creeping shrubs to small trees in Caprifoliaceae that exhibits a wide disjunct distribution in Eurasia, North America and Mexico. Most taxa of the subfamily occur in eastern Asia and Mexico but the monospecific genus Linnaea has a circumboreal to north temperate distribution. In this study, we conducted phylogenetic and biogeographic analyses for Linnaeoideae and its close relatives based on sequences of the nuclear ribosomal ITS and nine plastid (rbcL, trnS-G, matK, trnL-F, ndhA, trnD-psbM, petB-D, trnL-rpl32 and trnH-psbA) markers. Our results support that Linnaeoideae is monophyletic, consisting of four eastern Asian lineages (Abelia, Diabelia, Dipelta and Kolkwitzia), the Mexican Vesalea, and Linnaea. The Mexican Vesalea was formerly placed in Abelia, but it did not form a clade with the eastern Asian Abelia; instead Vesalea and Linnaea are sisters. The divergence time between the eastern Asian lineages and the Mexican Vesalea plus the Linnaea clade was dated to be 50.86 Ma, with a 95% highest posterior density of 42.8 Ma (middle Eocene) to 60.19 Ma (early Paleocene) using the Bayesian relaxed clock estimation. Reconstructed ancestral areas indicated that the common ancestor of Linnaea plus Vesalea may have been widespread in eastern Asia and Mexico or originated in eastern Asia during the Eocene and likely migrated across continents in the Northern Hemisphere via the North Atlantic Land Bridges or the Bering Land Bridge. The Qinling Mountains of eastern Asia are the modern-day center of diversity of Kolkwitzia-Dipelta-Diabelia clade. The Diabeliaclade became highly diversified in Japan and eastern China. Populations of Diabelia serrata in Japan and eastern China were found to be genetically identical in this study, suggesting a recent disjunction across the East China Sea, following the last glacial event.

Prunus subgenus Padus is a group with a wide distribution in temperate eastern Asia and eastern North America with one species extending to Europe and one to Central America. Phylogenetic relationships of subgenus Padus were reconstructed using sequences of nuclear ribosomal ITS, and plastid ndhF gene, and rps16 intron and rpl16 intron. Prunus subgenus Padus is shown to be polyphyletic. Taxa of subgenus Padus and subgenus Laurocerasus are highly intermixed in both the ITS and the plastid trees. The results support two disjunctions between eastern North America and Eurasia within the Padus group. One disjunction is between Prunus virginiana of eastern North America and P. padus of Eurasia, estimated to have diverged at 2.99 (95 % HPD 0.59-6.15)-4.1 (95 % HPD 0.63-8.59) mya. The other disjunction is between P. serotina and its Asian relatives. The second disjunction may have occurred earlier than the former one, but the age estimate is difficult due to the unresolved phylogenetic position of the P. serotina complex.

Anaphalis is the largest Asian genus in the tribe Gnaphalieae (Asteraceae) and has its greatest species diversity in the eastern Himalayas. The nuclear internal and external transcribed spacers were sequenced for Anaphalis species, with an emphasis on the eastern Himalayan taxa to examine the monophyly and construct the phylogenetic relationships of and within the genus. The results suggest that all species of Anaphalis are nested with Helichrysum, showing a close relationship with a Mediterranean-Asian group of Helichrysum. Although the monophyly of Anaphalis is only weakly supported, two clades within the genus are well recognized, each consisting of two subgroups. The inferred phylogenetic relationships within Anaphalis correspond to the shape of leaf base, rather than the morphology of the capitula and phyllaries that are usually used for species delimitation and classification in the genus. All four subgroups of Anaphalis are common and diversified in the eastern Himalayas with multiple dispersals out of this region. The sole North American species of Anaphalis is best hypothesized to be the result of long-distance dispersal or overland migration via Bering land bridge from Asia. Our analyses suggest that the extant distribution of Anaphalis has most likely resulted one radiation into the eastern Himalayas followed by repeated independent dispersals and/or radiations mostly into eastern Asia but also into the western Himalayas, North America, and southeast Asia.

A cytological study was carried out for the first time on four populations of the only two species of Kelloggia (Rubiaceae), which occur disjunctly in eastern Asia (K. chinensis Franch.) and western North America (K. galioides Torr.). The consistent mitotic prophase chromosome condensation pattern and interphase nuclei type were determined for both species. The chromosome base number of the genus is suggested to be x = 11. The karyotype of 2n = 22 = 2x = 16m + 6sm was examined for both species. The karyotypical asymmetry of 1A and 2A was found in K. chinensis and K. galioides, respectively. According to the predominant evolutionary direction of karyotype asymmetry in angiosperms, K. galioides (2A) seems slightly more evolved than K. chinensis (1A). Our finding is consistent with the hypothesis of the Old World origin of Kelloggia based on molecular study.

Symplocarpus, Lysichiton, and Orontium (Orontioideae) are three of the few north temperate genera of the primarily tropical Araceae. Symplocarpus is disjunctly distributed in eastern Asia (3 spp.) and eastern North America (1 sp.); Lysichiton has an intercontinental discontinuous distribution in eastern Asia (1 sp.) and northwestern North America (1 sp.); and the monotypic Orontium is restricted to eastern North America. Phylogenetic analysis of the trnL-F and ndhF sequences supports (1) the monophyly of both Symplocarpus and Lysichiton, (2) the sister-group relationship of Symplocarpus and Lysichiton, and (3) the clade of Orontium, Symplocarpus, and Lysichiton. Although Symplocarpus shows a much wider disjunction than Lysichiton, the estimated divergence time of the former [4.49+/-1.69 or 6.88+/-4.18 million years ago (mya)] was similar to that of the latter (4.02+/-1.60 or 7.18+/-4.33 mya) based on the penalized likelihood and the Bayesian dating methods, respectively. Eastern Asia was suggested to be the ancestral area of the Symplocarpus-Lysichiton clade based on the dispersal-vicariance analysis. Our biogeographic results support independent migrations of Symplocarpus and Lysichiton across the Bering land bridge in the late Tertiary (Pliocene/late Miocene). Fossil evidence suggests Orontioideae dated back to the late Cretaceous in the temperate Northern Hemisphere (72 mya). The relative rate test shows similar substitution rates of the trnL-F sequences between the proto and the true aroids, although the latter has substantially higher species diversity. The proto Araceae perhaps suffered from a higher rate of extinction in the temperate zone associated with periods of climatic cooling in the Tertiary.