Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus.

Jun Wen; Stefanie Ickert-Bond

The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus–Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus–Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4 Ma, 95% HPD: 32.6–48.6 Ma), then migrated to Eurasia in the late Eocene (37.3 Ma, 95% HPD: 30.9–45.1 Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism.

Molecular Phylogenetics and Evolution 95 (2016) 217–228 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus q Xiu-Qun Liu a, Stefanie M. Ickert-Bond b, Ze-Long Nie c, Zhuo Zhou d, Long-Qing Chen a, Jun Wen e,⇑ a Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA c Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China d Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China e Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA b a r t i c l e i n f o Article history: Received 10 November 2014 Revised 31 July 2015 Accepted 13 October 2015 Available online 3 November 2015 Keywords: Ampelocissus Vitis Grapes Vitaceae Biogeography a b s t r a c t The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus–Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus–Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4 Ma, 95% HPD: 32.6–48.6 Ma), then migrated to Eurasia in the late Eocene (37.3 Ma, 95% HPD: 30.9–45.1 Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism. Ó 2015 Elsevier Inc. All rights reserved. 1. Introduction The grape family (Vitaceae) has been widely recognized for its agronomic and economic importance as sources of grapes, wine, and raisins (Wen, 2007). It includes about 15 genera and ca. 900 species mostly in pantropical regions of Asia, Africa, Australia, the Neotropics, and the Pacific islands, with a few genera (Vitis L., Parthenocissus Planch. and Ampelopsis Michx.) in temperate regions of the Northern Hemisphere (Wen, 2007; Wen et al., 2007, 2013a, 2014). The phylogeny of Vitaceae has caught the attention of several teams of workers in recent years (Ingrouille et al., 2002; Liu et al., 2013; Lu et al., 2013; Ren et al., 2011; Rodrigues et al., q This paper was edited by the Associate Editor Jocelyn C. Hall. ⇑ Corresponding author. Fax: +1 202 786 2563. E-mail address: wenj@si.edu (J. Wen). http://dx.doi.org/10.1016/j.ympev.2015.10.013 1055-7903/Ó 2015 Elsevier Inc. All rights reserved. 2014; Rossetto et al., 2002, 2007; Soejima and Wen, 2006; TriasBlasi et al., 2012; Wen et al., 2007, 2013c). The family is morphologically unique, especially in having leaf-opposed tendrils, an unusual axile placentation with incompletely fused septa in a bicarpellate gynoecium, multicellular, stalked, caducous spherical structures known as ‘‘pearl” glands on various organs of the plant, and a suite of unique seed characters (Chen and Manchester, 2011; Gerrath and Poluszny, 2007; Ickert-Bond et al., 2014; Süssenguth, 1953; Wen, 2007; Wilson and Posluszny, 2003; Zhang et al., 2015). Several studies focused on the relationship of the economically important genus Vitis as well as other genera in Vitaceae. Ingrouille et al. (2002) suggested that Vitis formed a clade with Cayratia Juss., Cyphostemma (Planch.) Alston, Parthenocissus and Tetrastigma (Miq.) Planch., but the result was based on a limited number of species (20 species) and markers (only plastid rbcL) sampled. In the context of resolving Cissus phylogeny, Rossetto et al. (2002) 218 X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 reported that Vitis was associated with several Cissus species endemic to Australia. Rossetto et al. (2007) later concluded that these few Australian Cissus species were intermediate between Vitis and Ampelopsis mainly based on review of Australian Vitaceae. Soejima and Wen (2006) resolved five major clades of the family based on three chloroplast markers for 37 taxa. Vitis was shown to form a clade with Ampelocissus, Nothocissus and Pterisanthes, which formed the Ampelocissus–Vitis clade. This clade was strongly supported by the nuclear GAI1 sequences with 95 Vitaceae taxa sampled (Wen et al., 2007) and by three chloroplast markers based on 114 samples representing 12 genera (Ren et al., 2011). This clade was also strongly supported by five plastid markers based on 174 samples (Liu et al., 2013) and by sequences of 417 orthologous genes extracted from the transcriptome data of 15 species of Vitaceae (Wen et al., 2013c). So far, the Ampelocissus–Vitis clade has been confirmed to be composed of four genera, but the phylogenetic relationships within the clade have not been well resolved. Vitis includes ca. 70 species mostly in the temperate regions of the Northern Hemisphere (Chen et al., 2007; Moore and Wen, in press; Wen, 2007; Zecca et al., 2012). Several recent studies have reconstructed the phylogeny and/or hypothesized on the origin of Vitis (Miller et al., 2014; Péros et al., 2011; Tröndle et al., 2010; Wan et al., 2013; Zecca et al., 2012). Ingrouille et al. (2002) and Pelsy (2007) reported that Vitis was paraphyletic, whereas later studies supported its monophyly (Soejima and Wen, 2006; Tröndle et al., 2010; Wan et al., 2013; Wen et al., 2007; Zecca et al., 2012). Two subgenera of Vitis have been commonly recognized. Subgenus Vitis includes the majority of species with a wide distribution in the Northern Hemisphere, and subg. Muscadinia Planch. (2 species) is restricted to the southeastern United States, the West Indies and Mexico (Brizicky, 1965; Wen, 2007). The recognition of the two distinct subgenera is still debated (Zecca et al., 2012). While some phylogenetic analyses (Ingrouille et al., 2002; Pelsy, 2007) did not retain two separate clades, others robustly supported the placement of subg. Muscadinia as sister to subg. Vitis (Aradhya et al., 2008; Tröndle et al., 2010; Wan et al., 2013; Wen et al., 2007; Zecca et al., 2012). The phylogenetic relationships within subg. Vitis remain controversial. Galet (1988) classified 59 species of subg. Vitis into 11 series mainly based on morphological traits but also included habitat and biogeography. Galet’s classification scheme was partly supported by Péros et al. (2011) and Wan et al. (2013), but strongly rejected by Zecca et al. (2012) based on molecular data. Recent phylogenetic reconstructions reflected intercontinental disjunctions of the subgenus, but criticized a strict correspondence between phylogenetic and geographic groups (Aradhya et al., 2008; Di Gaspero et al., 2000; Pelsy, 2007; Tröndle et al., 2010; Zecca et al., 2012). In fact, the species delimitation within subg. Vitis is difficult and questioned due to hybridization or clinal variation within species (Comeaux et al., 1987; Moore, 1991; Péros et al., 2011; Wan et al., 2013; Zecca et al., 2012). Péros et al. (2011) suggested that subg. Vitis originated in Asia, and then dispersed to Europe and North America based on the ancestral chloroplast haplotypes. Zecca et al. (2012), however, questioned the inference and pointed out that the North American species might be older than the Asian ones, but the origin of Vitis was inconclusive based on chloroplast and the nuclear RPB2 gene sequences. Wan et al. (2013) argued for the origin of Vitis in North America, with subsequent migration to Asia and Europe. Ampelocissus includes ca. 95 species mostly from Africa, tropical Asia, and Australia, with only six species known from Central America (Chen and Manchester, 2007; Galet, 1967; Lombardi, 1997, 1999, 2000, 2005; Planchon, 1887; Süssenguth, 1953; Wen, 2007). The genus is characterized by inflorescences subtended by a tendril, a prominent floral disc usually with ten linear marks on its side, and the frequent association of rusty arachnoid hairs in young parts of the plant (Chen and Manchester, 2007). Based on inflorescence structure as well as leaf and seed morphology, Planchon (1887) recognized four sections, viz. sect. Euampelocissus Planch. (=sect. Ampelocissus), sect. Nothocissus (Miq.) Planch., sect. Kalocissus (Miq.) Planch. and sect. Eremocissus Planch. (Wen, 2007). Latiff (2001a) recognized a new section (sect. Ridleya Latiff) in which the inflorescence branches of the species became flattened similar to the lamellae of the Pterisanthes inflorescence (Latiff, 1982a). Nothocissus was elevated from sect. Nothocissus of Ampelocissus by Latiff (1982b). Nothocissus was initially monotypic, with only N. spicifera (Griff.) Latiff (Latiff, 1982b), and was similar to Ampelocissus sect. Kalocissus from the Malesian region in its floral structure and seeds (extremely rugose) (Latiff, 1982b). Latiff (2001b) expanded the generic concept of Nothocissus and transferred five species of Cissus (C. hypoglauca A. Gray, C. sterculiifolia (F. Muell. ex Benth.) Planch., C. penninervis F.v. Muell., C. acrantha Lauterb. and C. behrmannii Lauterb.) from Papua New Guinea and Australia to Nothocissus. However, recent studies cast doubt on three of these new combinations from Australia based on inflorescence morphology (Chen and Manchester, 2007) and molecular data (Rossetto et al., 2002, 2007; J. Wen, unpublished). Chen and Manchester (2007, 2011) recognized that the seeds of three Australian species (C. hypoglauca, C. penninervis and C. sterculiifolia) were not similar to those of N. spicifera. Liu et al. (2013) showed that the Australian C. hypoglauca formed a clade with the Neotropical C. trianae Planch. and another Australian species C. antarctica Vent., rather than showing a close relationship with N. spicifera. These studies indicate Nothocissus as defined by Latiff (1982b, 2001b) is clearly not monophyletic. Pterisanthes (ca. 20 species) from the Malay Peninsula, Borneo, Sumatra, Java, the Philippines, and peninsular Thailand, has seeds very similar to those of Ampelocissus, but is characterized by the unusual applanate or laminar structure of its inflorescence (Chen and Manchester, 2007; Latiff, 1982c; Wen, 2007; Ickert-Bond et al., 2015). The morphological similarity between Ampelocissus, Nothocissus and Pterisanthes has long been recognized (reviewed in Ickert-Bond et al., 2015; Chen and Manchester, 2007; Latiff, 1982c), and recent molecular data have shown that Nothocissus and Pterisanthes are nested within Ampelocissus (Liu et al., 2013; Ren et al., 2011; Soejima and Wen, 2006; Wen et al., 2007). Chen and Manchester (2007) designated Ampelocissus, Nothocissus and Pterisanthes as Ampelocissus s.l, which is distinguished from all other genera in Vitaceae by its seeds with long, parallel ventral infolds and a centrally positioned oval chalazal scar (Chen and Manchester, 2011). In the context of inferring the origin of Vitis, previous studies (e.g., Péros et al., 2011; Wan et al., 2013; Zecca et al., 2012) had very limited sampling of non-Vitis taxa in Vitaceae. We herein expand the sampling scheme in the closely related genera of Vitis and employ sequences of five plastid (rps16, trnL-F, atpB-rbcL, trnH-psbA and trnC-petN) and two nuclear (GAI1 and ITS) markers. The objectives of this study are to: (1) resolve the phylogenetic relationships within the Ampelocissus–Vitis clade; and (2) hypothesize the origin of Vitis in a broader phylogenetic framework. 2. Materials and methods 2.1. Sampling, DNA isolation and sequencing The study sampled 111 accessions representing the Ampelocissus–Vitis clade including 70 accessions of Vitis (38 spp.), 31 of Ampelocissus (20 spp.), eight of Pterisanthes (5 spp.) and two of Nothocissus (1 sp.), and generated sequences for five plastid (trnLF, the rps16 intron, atpB-rbcL, trnH-psbA and trnC-petN) and two X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 nuclear (GAI1 and ITS) markers (Table S1). The sampling covers the geographic and morphological diversity of the clade. Six species of Parthenocissus were selected as outgroup of the clade, as the genus had been shown to be sister to the Ampelocissus–Vitis clade (Ren et al., 2011; Wen et al., 2013c). In the dating analysis, we also used 55 representative taxa of other genera in Vitaceae and Leeaceae (Leea van Royen ex L.) as the outgroup of Vitaceae. Total DNAs were extracted from silica gel dried leaves using the DNeasy Plant Mini Kit (QIAGEN, California, USA) following the manufacturer’s protocol. The sequences of five plastid DNA markers (trnL-F, rps16, atpB-rbcL, trnH-psbA, and trnC-petN) were amplified and sequenced following previous methods (Anderssons and Rova, 1999; Chen et al., 2011a; Lee and Wen, 2004; Oxelman et al., 1997; Ren et al., 2011; Soejima and Wen, 2006; Taberlet et al., 1991). For the nuclear GAI1 gene, PCRs were first carried out using primers (1F, 1R, 2F, and 2R) of Wen et al. (2007) to amplify GAI1 sequences. In the cases where amplification was not successful, we designed several pairs of primers to amplify the gene. These were forward primers 83F (50 -GCT TCC GAG ACT GTT CAT TAC-30 ), 350F (50 -GGT AAG GCT CTY TAT TCC CAT-30 ), or 496F (50 -TGA AGC CCA CAA CTT CAG CT-30 ) and reverse primer 1520R (50 -CTT CGC AGG CCA CCA CGT T-30 ). For ITS, PCR amplification used the forward primers N-nc18S10 and ITS1 and reverse primers C26A and ITS4 (Wen and Zimmer, 1996; White et al., 1990). For GAI1 and ITS, most amplification products were sequenced directly after purification using the QIAquick PCR Purification kit (QIAGEN, California, USA). For those PCR products that were weakly amplified and difficult to be sequenced directly, we used the QIAGEN PCR Cloning Kit (QIAGEN, California, USA) to clone and sequence at least eight clones. If more than one copy was isolated in one sample, we first constructed a phylogeny including all the copies. If multiple copies from the same sample grouped together, one copy was randomly selected in further analysis. DNA sequences were assembled using the program Sequencher version 5.0.1 (Gene Codes Corp., Ann Arbor, Michigan, USA). 2.2. Sequence alignment and phylogenetic analysis Sequence alignment was initially performed using the program MUSCLE 3.8.31 (Edgar, 2004) in multiple alignment routine, followed by manual adjustment with the program Se-Al version 2.0a11 (Rambaut, 2002). Phylogenetic trees of the plastid data and the combined matrix of the five plastid and two nuclear markers were reconstructed using maximum parsimony (MP; Fitch, 1971), maximum likelihood (ML) and Bayesian inference (BI) (Mau et al., 1999; Rannala and Yang, 1996). MP analyses were conducted under the heuristic search option using 10 random stepwise additions and tree-bisec tion–reconnection (TBR) branch swapping in PAUP⁄ version 4.0 b10 (Swofford, 2003). Zero-length branches were collapsed and gaps were treated as missing data or coded as simple indels (Simmons and Ochoterena, 2000) using the program SeqState (Müller, 2005). Parsimony bootstrap analyses (Felsenstein, 1985) with 1000 replicates were subsequently performed under the option fast and stepwise addition to evaluate the robustness of the MP trees. MrModeltest 2.3 (Nylander, 2004) was used to determine the best available model for nucleotide substitutions using the Akaike Information Criterion (AIC). The chloroplast genome is generally considered as one unit without combination although there had been reports of recombination in the chloroplast genome (Stein et al., 1986). Therefore, we combined the five chloroplast data (rps16, trnL-F, atpB-rbcL, trnH-psbA and trnC-petN). The most appropriate nucleotide substitution model (GTR + G) was determined by MrModeltest 2.3 using AIC for each of five chloroplast data and the combined dataset. A partitioned Bayesian analysis of the five 219 chloroplast data was then implemented by applying the GTR + G model as determined above. The SYM + G and GTR + I + U models were determined as the most appropriate nucleotide substitution ones for ITS and GAI1 data, respectively. In the following ML and BI analysis the substitution models and parameters were adjusted according to the estimates of MrModeltest. Bayesian inference was used to estimate the posterior probabilities of phylogenetic trees by employing an analysis of 5 million generations Metropolis-coupled Markov chain Monte Carlo (MCMC) with MrBayes version 3.1.2 (Huelsenbeck and Ronquist, 2001). For analyses of the concatenated datasets, all datasets were partitioned with unlinked substitution models as estimated before. The sampling rate of the trees was 1000 generations. Runs were repeated twice to confirm results. After discarding the trees saved prior to this point as burn-in, the remaining trees were loaded into PAUP⁄, and a 50%-majority rule consensus tree was computed to obtain posterior probabilities of the clades. Results were considered reliable once the effective sampling size (EES) for all parameters exceeded 200 as suggested by the program manual (Drummond et al., 2007). 2.3. Bayesian dating and fossil calibration Representatives of the entire grape family plus Leea were sampled to help date the ages with both fossils and secondary calibrations in Vitales. We used the Bayesian dating method based on a relaxed-clock model to estimate divergence times (Drummond et al., 2006; Thorne et al., 1998; Thorne and Kishino, 2002). The Bayesian coalescent approach to estimate the times and their credibility intervals was implemented in the Program BEAST 1.7.0 (Drummond and Rambaut, 2007), which employed a Bayesian MCMC to co-estimate topology, substitution rates and node ages. After optimal operator adjustment as suggested by the output diagnostics from several preliminary BEAST runs, two final independent runs (each 50 million generations) were performed on a cluster of Mac XServes for analysis of biological data at the Smithsonian Institution. Convergence between runs was assessed with MrBayes using Tracer version 1.5. After discarding the first 10% samples as burn-in, the trees and parameter estimates from the two runs were combined by LogCombiner 1.6.1 (Drummond and Rambaut, 2007). Results were considered reliable once the effective sample size (ESS) for all parameters exceeded 200 as suggested by Drummond et al. (2007). The samples from the posterior were summarized on the posterior probabilities on its internal nodes (Drummond et al., 2007) using the program TreeAnnotator version 1.6.1 (Drummond and Rambaut, 2007) with posterior probability limit set to 0.5 and summarizing mean node heights. These were visualized using the program FigTree version 1.2.2 (Drummond et al., 2007). Mean and 95% highest posterior density (HPD) of age estimates were obtained from the combined outputs using Tracer version 1.5. In the Paleobiological Database (2010), fossils with a Vitaceae affinity date back to as early as the early Cenomanian (99.6– 93.5 Ma), but the taxonomic affinities of the oldest fossils are very controversial (Chen and Manchester, 2007; Chen, 2009; Manchester et al., 2013). Vitaceae fossils are available from sediments from the late Cretaceous to the Pleistocene and include leaves, pollen, stems, and seeds (Chen and Manchester, 2007; Greguss, 1969; Manchester et al., 2013; Tiffney and Barghoorn, 1976; Wheeler and Lapasha, 1994). Nevertheless, the seed record of the family is potentially more informative for addressing questions of evolutionary and phytogeographic divergence, because these fossils can be differentiated at the generic level (Chen, 2009; Chen and Manchester, 2007, 2011). The oldest confirmed Vitaceae fossil (66 million years old) is Indovitis chitaleyae Manch- 220 X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 ester, Kapgate & J. Wen from the late Cretaceous of India (Manchester et al., 2013). But it seems not suitable for our calibration strategy due to the two alternative phylogenetic positions for Indovitis either sister to the Ampelocissus–Vitis clade or sister to the Ampelopsis–Clematicissus–Rhoicissus clade (Manchester et al., 2013). The second oldest confirmed seed fossil is undoubtedly assigned to Ampelocissus s.l. (A. parvisemina Chen & Manchester) and dates back to the late Paleocene (56.8–62.0 Ma) in North Dakota of North America (Chen and Manchester, 2007). We used Ampelocissus parvisemina as our first fossil calibration to estimate the divergence time of Vitis, similar to the dating analyses of Parthenocissus (Nie et al., 2010), Tetrastigma (Chen et al., 2011b), Ampelopsis (Nie et al., 2012), Cissus (Liu et al., 2013), and Vitis (Zecca et al., 2012) in Vitaceae. Because the fossil seed was assigned with certainty to the genus Ampelocissus (Chen and Manchester, 2007), Liu et al. (2013) assigned it as representing an early member of the Ampelocissus–Vitis clade. We ran the analysis constraining the crown age of this clade, with a lognormal prior distribution (mean: 58.5 Ma; log (stdev: 0.03); offset: 0 Ma; mean in real space) approximately corresponding to the time span of the late Paleocene. Fossil seeds of Vitis macrochalaza Tiffney from the early Miocene of the Brandon Lignite in Vermont, northeastern North America, are strikingly similar to those of the modern species Vitis rotundifolia Michx. (Tiffney, 1979, 1994; Tiffney and Barghoorn, 1976). Thus the fossil was assigned to the early members of subg. Muscadinia and used as the second calibration point of the Vitis divergence. We fixed the fossil to the crown of subg. Muscadinia with a lognormal prior distribution (mean: 20 Ma; log (stdev: 0.07); offset: 0 Ma; mean in real space) approximately corresponding to the upper and lower bounds of the early Miocene. The late Eocene Vitis glabra Chandler from the lower Bagshot beds of the London Clay of southern England, is the most reliable among the earliest fossils of subg. Vitis based on the fossil seed morphology described in the literature (Chandler, 1957, 1960, 1961, 1962, 1963, 1964; Collinson, 1983; Mai, 2000; Manchester, 1994; Miki, 1956; Reid and Chandler, 1933; Tiffney and Barghoorn, 1976). So, this fossil was assigned to the early members of subg. Vitis and used as the third calibration point of the Vitis divergence. We ran the analysis constraining the crown age of subg. Vitis with a lognormal prior distribution (mean: 35 Ma; log (stdev: 0.02); offset: 0 Ma; mean in real space) approximately corresponding to the time span of the late Eocene. Gong et al. (2010) reported several fossil Vitis seeds including three morphotaxa from the Gray fossil site in northeastern Tennessee (7–4.5 Ma, latest Miocene to earliest Pliocene). Based on their preservation, the fossil seeds were included as members of subg. Vitis and described as V. grayensis Gong, Karsai & Liu, V. lanatoides Gong, Karsai & Liu and V. latisulcata Gong, Karsai & Liu, most closely comparable to modern V. balanseana Planch. and V. thunbergii Sieb. & Zucc. from Asia, modern V. lanata Roxb. from Asia, and modern V. labrusca L. from North America, respectively (Gong et al., 2010). Since there is uncertainty of the phylogenetic position of the fossil species from Tennessee, we did not include these fossil seeds as calibration points. Herrera et al. (2012) described a new genus Saxuva Herrera, Manchester & Jaramillo based on Vitaceae fossil seeds from the late Eocene of Panama. Its type species S. draculoidea Herrera, Manchester & Jaramillo was described as having tetramerous flowers. The taxon exhibited characters seen in three modern genera Cayratia, Cissus and Cyphostemma (Herrera et al., 2012) which were placed in different clades in the Vitaceae phylogeny (Liu et al., 2013; Wen et al., 2013c), and thus it did not seem suitable for our calibration strategy. For the root age of Vitaceae, Nie et al. (2010) fixed the split between Vitaceae and Leea as 85 ± 4.0 Ma based on the estimated age of 78–92 Ma by Wikström et al. (2001). Magallón and Castillo (2009) reported a pre-Tertiary origin at 90.65–90.82 Ma for Vitaceae. The estimated ages from Magallón and Castillo (2009) and Wikström et al. (2001) are close, but the latter was criticized for using nonparametric rate smoothing and for calibrating the tree using only a single calibration point (Nie et al., 2012). Bell et al. (2010) suggested a time ranging from 48 to 65 Ma for the stem age of Vitaceae. Although their estimates were based on 36 fossil calibrations in dating 567 taxa of angiosperms, they obviously underestimated the age for Vitaceae because the ages were younger than the age suggested by fossil evidence (e.g., in Chen and Manchester, 2007). We herein used the estimate from Magallón and Castillo (2009) and set the normal prior distribution of 90.7 ± 1.0 Ma for the stem age of the family (Liu et al., 2013). 2.4. Ancestral area reconstruction To reconstruct the geographic origin of Vitis, a dispersalvicariance analysis was conducted (Ronquist, 1997) using the software RASP v2.1 (Reconstruct Ancestral State in Phylogenies, available online at http://mnh.scu.edu.cn/soft/blog/RASP), a modified version of S-DIVA (Statistical Dispersal-Vicariance Analysis; Yu et al., 2010) using a Bayesian binary MCMC (BBM) approach. The method calculates the optimized areas over a set of trees, thus taking into account topological uncertainty (Thiv et al., 2011). We used the 7500 trees retained from the BEAST analysis of the combined data set. The ancestral area of Vitis was also reconstructed by maximum likelihood (ML) optimization in Lagrange version 20120508 (Ree and Smith, 2008). The program Lagrange not only finds the most likely ancestral area at a node and the split of the areas in the two descendant lineages, it also calculates the probabilities of these most-likely areas at each node (Ree and Smith, 2008), using an ultrametric tree combining the ML topology with internal node age estimated from a BEAST analysis based on the combined data set. In our case, all combinations of areas were allowed in the adjacency matrix, and baseline rates of dispersal and local extinction were estimated. The maximum number of areas in the ancestral ranges was limited to two in RASP and Lagrange, as no species of Vitaceae is distributed in more than two areas of endemism. Four areas of endemism were defined according to the distribution of the clade of grapes and their allies: A, Southern and eastern Asia, Malesia and Northern Australasia; B, North and Central America, and the northern border of South America (with Vitis tiliifolia extended southward); C, Sub-Saharan Africa and Madagascar; and D, Mediterranean and Western Asia (only Vitis vinifera). 3. Results 3.1. Phylogenetic analyses We used the combined matrix of all the plastid data (rps16, trnL-F, atpB-rbcL, trnH-psbA and trnC-petN) in our analysis. The aligned matrix of combined plastid DNA data has 6701 characters including 1312 parsimony-informative sites (consistency index CI = 0.60, retention index RI = 0.82). The aligned ITS data matrix comprises 927 characters including 533 parsimony-informative sites (CI = 0.39, RI = 0.64). The aligned GAI1 data matrix has 1493 characters including 454 parsimony informative sites (CI = 0.61, RI = 0.83). Two datasets of ITS and GAI1 resulted in five major clades (A., B., C., D., E.; Figs. S2 and S3) with high values of Bayesian posterior probabilities (PP > 0.95) and MP bootstrap support (BS > 0.50). The combined chloroplast datasets support the four clades (A., C., D., E.), while clade B is not supported (Fig. S1): A. acapulcensis (Kunth) Planch. is sister to clade A with low supporting values (BS < 50%, PP = 0.74), and A. javalensis (Seemann) Stevens X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 & Pool is sister to clade E with low supporting values (BS < 50%, PP = 0.90), respectively. Two clades show low PP and BS values: (1) clade E based on chloroplast sequences (BS < 50%, PP = 0.66, Fig. S1), and (2) clade A based on ITS sequence data (BS < 50%, PP = 0.77, Fig. S2). All of the three datasets (ITS, GAI1 and the combined plastid matrix) support that clade A includes three subclades, and that clade E includes two subclades (Figs. S1–S3), except for the ITS dataset due to missing sequences (Fig. S2). We combined these three datasets based on the very similar topologies among the major clades in the current case. The concatenated data clearly show improved phylogenetic resolution of the major clades (PP = 1.00, BS > 85%) (Fig. 1). The combined matrix of the three datasets is 8491 bp in length, containing 2299 parsimony-informative sites. Trees generated with different methods (MP, ML, and BI) are consistent with respect to the Ampelocissus–Vitis clade. Therefore, only the BI strict consensus tree with MP bootstrap support (BS) and Bayesian posterior probabilities (PP) is shown (Fig. 1). The parsimony search of the combined dataset yielded more than 100,000 most parsimonious trees (CI = 0.51, RI = 0.76). The strict consensus tree of the combined dataset corresponds to the majority-rule consensus of 7500 trees (10,000 trees minus 2500 as burn-in) derived from the BI analysis (Fig. 1). In the combined analysis of cpDNA, GAI1 and ITS data, the Ampelocissus–Vitis clade is well supported with BS = 100% and PP = 1.00. Five clades (Fig. 1) are contained. Clade A (BS = 96%; PP = 1.00) consists of Vitis and the New World Ampelocissus erdvendbergiana Planch., with the latter sister to the former. Ampelocissus erdvendbergiana forms a polytomy with both subclades of Vitis in GAI1 analyses (Fig. S3). Vitis is supported as a monophyletic genus (BS = 84%; PP = 1.00). Within Vitis, subg. Muscadinia (BS = 97%; PP = 1.00) and subg. Vitis (BS = 91%; PP = 1.00) are each supported to be monophyletic. Within subg. Vitis, two groups are weakly supported, corresponding to their biogeographic distribution in the New World and Eurasia, respectively (Fig. 1). Ampelocissus is paraphyletic, with Vitis, Nothocissus and Pterisanthes nested within it (Fig. 1). Taxa of Ampelocissus are primarily placed in three clades (B, C and D; Fig. 1) except for the species of A. erdvendbergiana from the New World. Clade B consists of two New World species, A. javalensis and A. acapulcensis, forming a well supported clade (BS = 90%; PP = 1.00) based on the combined data (Fig. 1). These results are identical to the GAI1 result (Fig. S3) with two exceptions, A. javalensis and A. acapulcensis. But A. javalensis and A. acapulcensis have different placements in the chloroplast tree with low support (Fig. S1): A. javalensis is sister to clade E (BS < 50%, PP = 0.90), and A. acapulcensis is sister to clade A (BS < 50%, PP = 0.74), respectively. We failed to obtain the ITS sequence of A. javalensis (Fig. S2). Clade C (BS = 94%; PP = 1.00) consists of the majority of the Asian Ampelocissus species (corresponding to Ampelocissus sect. Kalocissus) in which Pterisanthes from tropical Asia is nested. Clade D (BS = 100%; PP = 1.00) includes one species, N. spicifera, which is sister to clade C (BS = 94%; PP = 1.00). Clade E includes the African Ampelocissus with several Asian species (BS = 88%, PP = 1.00), and is divided into two subclades (BS = 51%, PP = 1.00; and BS = 55%; PP = 1.00 respectively). Clade E roughly corresponds to Ampelocissus sect. Ampelocissus (except for species from the New World). 3.2. Divergence times of the Ampelocissus–Vitis clade Bayesian estimation of divergence times of the Ampelocissus– Vitis clade is presented in Fig. 2. The clade is estimated to have diverged from the closest relative in Vitaceae (the ParthenocissusYua clade) in the late Cretaceous (70.5 Ma, 95% HPD: 57.9– 82.0 Ma; node 1 in Fig. 2). The Mexican species A. erdvendbergiana is estimated to have split from the Vitis clade in the late Eocene 221 (39.4 Ma, 95% HPD: 32.6–48.6 Ma; node 3 in Fig. 2). The split of the two subgenera of Vitis is estimated to have occurred in the late Eocene (37.3 Ma, 95% HPD: 30.9–45.1 Ma; node 3 in Fig. 2). 3.3. Biogeographic origin of Vitis The ancestral area of Vitis is reconstructed to be in the New World according to the two analyses of RASP (B (0.69)/AB (0.31), posterior probabilities = 1.00, node a in Fig. 3) and Lagrange (B|B and B|AB, with 0.83 and 0.14 relative probabilities, respectively, node a in Fig. 3). The ancestral area of subg. Vitis is inferred in the New World by RASP (B (0.72)/AB (0.28), posterior probabilities = 0.83, node b in Fig. 3) and Lagrange (B|B and B|AB, with 0.77 and 0.18 relative probabilities, respectively, node b in Fig. 3). 4. Discussion 4.1. Phylogenetic relationships Our phylogenetic results support five major clades (A., B., C., D., E; Fig. 1) within the Ampelocissus–Vitis clade in Vitaceae. Clade A consists of Vitis and Ampelocissus erdvendbergiana (BS = 96%; PP = 1.00; Fig. 1), which shows a disjunct distribution in the Neotropics, Eurasia and North America. Taxa in clade A bear cordiform seeds with short, linear, and parallel ventral infolds with round to linear cavities (Chen and Manchester, 2007, 2011). Clade A is divided into three subclades (Fig. 1). The first subclade includes only one species, A. erdvendbergiana from Central America (BS = 100%; PP = 1.00; Fig. 1). This study suggests that A. erdvendbergiana is most closely related to Vitis, and confirms that Vitis is monophyletic, consisting of two subgenera. The second subclade includes the only two species of Vitis subg. Muscadinia: V. popenoei J.H. Fennel from Mexico and V. rotundifolia Michx. from the southeastern U.S.A. (BS = 97%; PP = 1.00; Fig. 1). Taxa of subg. Muscadinia have 40 chromosomes, simple tendrils, larger fruits and seeds with longer ventral infolds than the rest of species in Vitis (Chen and Manchester, 2011). The third subclade consists of subg. Vitis with 38 chromosomes, and bifurcate or trifurcate tendrils. Subg. Vitis includes species from temperate North America (BS < 50%; PP = 1.00) and their sister group from temperate Asia and Europe (BS < 50%; PP = 0.71; Fig. 1). Our result confirms the biogeographic disjunctions of subg. Vitis between North America and Eurasia (Miller et al., 2014; Péros et al., 2011; Tröndle et al., 2010; Zecca et al., 2012). Wan et al. (2013) suggested that the clades of Eurasian species were nested within the North American grade of subg. Vitis, but our result supports the sister relationships between the North American and Eurasian subclades (BS = 91%; PP = 1.00; Fig. 1) within subg. Vitis. Our resolution within subgen. Vitis is low, probably due to our marker choice, as well as recent divergences, hybridization among species, and clinal variation within species (Comeaux et al., 1987; Péros et al., 2011; Zecca et al., 2012). In our study, several species are not supported as monophyletic, because they may be more appropriately viewed as ecospecies or ecotypes rather than biological species (Zecca et al., 2012). The taxonomy of Vitis clearly needs to be critically assessed. Ampelocissus is paraphyletic (Figs. 1–3). Taxa in this genus are placed in three clades (B., C., E.; Fig. 1) except for A. erdvendbergiana. The three Central American Ampelocissus species do not form a clade (Fig. 1). Ampelocissus acapulcensis and A. javalensis constitute a clade B (BS = 90%; PP = 1.00; Fig. 1), whereas A. erdvendbergiana is sister to Vitis based on the combined data (Fig. 1). Clade B is strongly supported by the GAI as well (Fig. S3), but the cpDNA sequences do not resolve the clade (Fig. S1). The two species in clade B have oval or pyriform seeds with broad ventral infolds (Chen and Manchester, 2007). In fact, the phylogenetic positions 222 X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 Fig. 1. Phylogenetic relationships of grapes and their close allies using the combined datasets of chloroplast, ITS and GAI1 sequences based on the BI strict consensus cladogram with MP bootstrap support (numbers below branches) and Bayesian posterior probabilities (numbers above branches). Bold branches represent PP = 1.00 and BS > 90%. 223 X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 90.0 80.0 70.0 Cretaceous 60.0 50.0 Paleocene 40.0 Eocene 30.0 20.0 10.0 Miocene Oligocene 0.0 Plio 1 2 3 Vitis Age estimates [95% HPD] subg. Vitis 1 70.5 [57.9-82.0] Ma 2 39.4 [32.6-48.6] Ma 3 37.3 [30.9-45.1] Ma Cretaceous 90.0 80.0 Paleocene 70.0 60.0 Eocene 50.0 Miocene Oligocene 40.0 30.0 20.0 10.0 Ampelocissus-Vitis Clade subg. Muscadinia Parthenocissus-Yua Clade Leea guineensis W8684 Leea cuspidifera W9621 Ampelopsis cantoniensis Z350 Ampelopsis hypoglauca W8195 Ampelopsis cordata W9700 Rhoicissus tomentosa W10076 Rhoicissus digitata Gerrath s.n. Rhoicissus tridentata L11453 Clematicissus oppaca S11005 Clematicissus angustissima R2002 Cissus simsiana NW53805 Cissus granulosa W8611 Cissus striata ssp. argentina NW53854 Cyphostemma adenocaule L11459 Cyphostemma montagnacii W6672 Cyphostemma maranguense L11468 Cyphostemma simulans Gerrath s.n. Cyphostemma jiguu L11551 Cayratia acris W12183 Cayratia mollissima W8403 Cayratia pedata W7428 Cayratia japonica SH81847 Cayratia trifolia W10167 Cayratia maritima W10701 Tetrastigma obtectum NM454 Tetrastigma hemsleyarum W10792 Tetrastigma pachyphyllum W10919 Tetrastigma lanyuense W9404 Cissus trianae NW53942 Cissus hypoglauca W12185 Cissus antarctica W6685 Cissus floribunda W9463 Cissus sagittifera W9605 Cissus integrifolia L11475 Cissus adnata W10268 Cissus aralioide Aplin s.n. Cissus rotundifolia L11478 Cissus quadrangularis W7368 Cissus discolor W7468 Cissus cornifolia L11452 Cissus producta L11528 Cissus diffusiflora J1813 Cissus repanda W9027 Cissus gongylodes NW53777 Cissus erosa W8586 Cissus trifoliata W7287 Cissus biformifolia W7020 Cissus amazonica 2010-099 Cissus verticillata 2010-089 Yua thomsonii NM469 Yua austro-orientalis SIB1313 Parthenocissus vitacea NM394 Parthenocissus quinquefolia W8684 Parthenocissus heterophylla W10696 Parthenocissus chinensis NM455 Parthenocissus tricuspidata NM355 Parthenocissus suberosa NM358 Ampelocissus acapulcensis W8696 Ampelocissus javalensis W6920 Ampelocissus africana L11536 Ampelocissus obtusata L11590 Ampelocissus obtusata ssp. kirkiana Ampelocissus martini W7421 Ampelocissus arachnoidea W10290 Ampelocissus abyssinica 19971047 Ampelocissus elephantina W9646 Ampelocissus elephantina var. sph.W9640 Ampelocissus latifolia Akfandray Nothocissus spicifera W7513 Nothocissus spicifera W11675 Pterisanthes glabra W8394 Pterisanthes heterantha W11820 Ampelocissus thyrsiflora D870 Pterisanthes eriopoda W11717 Ampelocissus cinnamomea W11697 Pterisanthes eriopoda W11831 Pterisanthes stonei W8346 Ampelocissus floccosa W11686 Ampelocissus polystachya W11682 Ampelocissus elegans W11825 Ampelocissus gracilis W11684 Pterisanthes cissioides W11804 Ampelocissus ascendiflora W11822 Ampelocissus erdvendbergiana W8697 Ampelocissus erdvendbergiana W8708 Vitis rotundifolia W11087 Vitis popenoei W8724 Vitis mustangensis W9787 Vitis aestivalis W10428 Vitis arizonica W7260 Vitis labrusca W8652 Vitis tiliifolia W8674 Vitis tiliifolia W11894 Vitis riparia W7317 Vitis riparia W8658 Vitis cinerea var. helleri W9709 Vitis “hybrid” W10025 Vitis monticola W9746 Vitis cinerea var. floridana W10013 Vitis chunganensis W11406 Vitis davidii W9060 Vitis piasezkii W8031 Vitis piasezkii W9036 Vitis mengziensis NM415 Vitis betulifolia W8217 Vitis menghaiensis NM405 Vitis davidii SH44231 Vitis menghaiensis W10636 Vitis bellula W11271 Vitis vinifera Vitis sinocinerea W9446 Vitis heyneana W10647 Vitis heyneana W9378 Vitis bellula W11434 Vitis bryoniifolia W11620 Vitis lanata W9197 Vitis jacquemontii NM670 Vitis pseudoreticulata W11403 Vitis wilsonii W11637 Vitis pseudoreticulata W11619 Plio 0.0Ma Fig. 2. Chronogram of Vitis based on the combined plastid and nuclear datasets inferred from BEAST. Blue bars represent the 95% highest posterior density credibility interval for node ages. Calibration points are indicated with stars. Estimated divergence times of grapes and their close allies are indicated at the nodes (nodes 1–3) using circles and the estimated ages are shown on the left. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) 224 X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 B|B(0.39) A|A(0.35) A|AB(0.10) A(0.54) AB(0.46) B|AB(0.94) AB(0.52) BC(0.46) AB(0.02) AB|B(0.83) B|B(0.31) AB(0.53) B(0.47) C|AC(0.93) C(0.51) AC(0.49) A|A(0.89) AC|A(0.10) AC(0.54) A(0.46) A|AC(0.87) A(0.51) AC(0.49) A|A(1.00) A(1.00) B|B(0.83) B|AB(0.14) B(0.69) AB(0.31) subg. Muscadinia a B|B(0.77) B|AB(0.18) b B(0.72) AB(0.28) Vitis subg. Vitis Vitis Ampelocissus Nothocissus Pterisanthes NALB LDD B|A(0.64) B|D(0.33) AB(0.96) BD(0.04) Yua thomsonii NM469 Yua austro-orientalis SIB1313 Parthenocissus vitacea NM394 Parthenocissus quinquefolia W8684 Parthenocissus heterophylla W10696 Parthenocissus chinensis NM455 Parthenocissus tricuspidata NM355 Parthenocissus suberosa NM358 Ampelocissus acapulcensis W8696 Ampelocissus javalensis W6920 Ampelocissus africana L11536 Ampelocissus obtusata L11590 Ampelocissus obtusata ssp. kirkiana Ampelocissus martini W7421 Ampelocissus arachnoidea W10290 Ampelocissus abyssinica 19971047 Ampelocissus elephantina W9646 Ampelocissus elephantina var. sph. W9640 Ampelocissus latifolia Akfandray Nothocissus spicifera W7513 Nothocissus spicifera W11675 Pterisanthes glabra W8394 Pterisanthes heterantha W11820 Ampelocissus thyrsiflora D870 Pterisanthes eriopoda W11717 Ampelocissus cinnamomea W11697 Pterisanthes eriopoda W11831 Pterisanthes stonei W8346 Ampelocissus floccosa W11686 Ampelocissus polystachya W11682 Ampelocissus elegans W11825 Ampelocissus gracilis W11684 Pterisanthes cissioides W11804 Ampelocissus ascendiflora W11822 Ampelocissus erdvendbergiana W8697 Ampelocissus erdvendbergiana W8708 Vitis rotundifolia W11087 Vitis popenoei W8724 Vitis mustangensis W9787 Vitis aestivalis W10428 Vitis arizonica W7260 Vitis labrusca W8652 Vitis tiliifolia W8674 Vitis tiliifolia W11894 Vitis riparia W7317 Vitis riparia W8658 Vitis cinerea var. helleri W9709 Vitis “hybrid” W10025 Vitis monticola W9746 Vitis cinerea var. flor idana W10013 Vitis chunganensis W11406 Vitis davidii W9060 Vitis piasezkii W8031 Vitis piasezkii W9036 Vitis mengziensis NM415 Vitis betulifolia W8217 Vitis menghaiensis NM405 Vitis davidii SH44231 Vitis menghaiensis W10636 Vitis bellula W11271 Vitis vinifera Vitis sinociner ea W9446 Vitis heyneana W10647 Vitis heyneana W9378 Vitis bellula W11434 Vitis bryoniifolia W11620 Vitis lanata W9197 Vitis jacquemontii NM 670 Vitis pseudoreticulata W11403 Vitis wilsonii W11637 Vitis pseudoreticulata W11619 Fig. 3. Ancestral area reconstruction of the Ampelocissus–Vitis clade based on RASP and Lagrange analyses. The tree was based on a 50% majority-rule consensus tree of a Bayesian Markov chain Monte Carlo (MCMC) analysis of the combined dataset. The four areas of endemism are: A, Southern and eastern Asia, Malesia and Northern Australasia (blue circle); B, Northern and Central America and Northern South America (pink circle); C, Sub-Saharan Africa and Madagascar (brown circle); and D, Mediterranean and Western Asia (black circle). Painted areas in the map represent distributions of different genera: green, Vitis; yellow, Ampelocissus; orange, Nothocissus; and red, Pterisanthes. Colored circles at the tip of the nodes in the tree indicate species distributions as seen in the map below. Results of Lagrange and RASP analyses were at the upper and lower sides of a short line, respectively. For the Lagrange results, a slash indicates the split of areas into two daughter lineages, i.e., left/right, where ‘‘up” and ‘‘down” are the ranges inherited by each descendant branch; the values in brackets represent relative probabilities. For the RASP ones, the values in brackets represent S-DIVA support. Nodes a and b in the tree show the ancestral areas of the different clades. Red and purple dashed arrows in the map indicate Vitis migration route via NALB or LDD between the New and the Old Worlds, respectively. X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 of the New World Ampelocissus species have been uncertain for a long time. Ampelocissus javalensis was placed in Vitis (Seemann, 1869), Cissus (Planchon, 1887) or Ampelocissus (Lombardi, 1999). Planchon (1887) treated A. acapulcensis and A. erdvendbergiana as members of sect. Ampelocissus, together with species from the Old World. Our results suggest that A. erdvendbergiana is perhaps best treated as a member of Vitis, and A. acapulcensis and A. javalensis should be placed in a new genus. Clade C consists of nine species of Ampelocissus and six species of Pterisanthes sampled from tropical Asia (BS = 94%; PP = 1.00; Fig. 1). These taxa have a paniculate thyrse of spikes or a thyrse with specialized lamellate inflorescence branches, mostly with sessile flowers (Ickert-Bond et al., 2015). The seeds of Asian Ampelocissus in clade C are oval, highly compressed dorsiventrally, smooth, flattened and with broad ventral infolds. The seeds of Pterisanthes are rotund and have cup-shaped and wide ventral infolds, which are very similar to those of Ampelocissus of clade C (Chen and Manchester, 2007). All taxa of Ampelocissus in clade C are distributed in the lowland forests of tropical Asia and correspond to sect. Kalocissus recognized by Planchon (1887). Our phylogenetic results support that Pterisanthes is nested within Asian Ampelocissus and has a very close relationship with Ampelocissus sect. Kalocissus (BS = 94%; PP = 1.00; Fig. 2). Pterisanthes differs from Ampelocissus morphologically mainly because of its unique lamellate inflorescence branches, but the similarities in seed morphology, petiole anatomy, indumentum types and differentiation of the primary branch of the inflorescence into tendrils show a close relationship with Ampelocissus species in clade C (also see Latiff, 1982c). Van Steenis and Bakhuizen van den Brink (1967) suggested that Pterisanthes might be an artificial genus consisting of an assemblage of Ampelocissus because the former might have originated from the latter via inflorescence specialization. Latiff (2001a, 2001b) recognized Ampelocissus sect. Ridleya, including three species (A. pterisanthella Ridley, A. complanata Latiff and A. madulidii Latiff), which showed flattened inflorescence branches simulating the lamellae of Pterisanthes (Latiff, 1982a, 1982d). However, we failed to sample the three species included in sect. Ridleya in our study. Our results show the polyphyly of Pterisanthes (Figs. 1–3), supporting the notion by van Steenis and Bakhuizen van den Brink (1967) on the artificial nature of Pterisanthes. We suggest new combinations need to be made to transfer these species of Pterisanthes to Ampelocissus. Clade D includes only Nothocissus spicifera (Fig. 1), which is sister to the clade containing most Asian Ampelocissus and Pterisanthes (BS = 94%; PP = 100; Fig. 1, Clade C). Previous abo vementioned studies (Chen and Manchester, 2007, 2011; Liu et al., 2013; Rossetto et al., 2007) indicated that Nothocissus as defined by Latiff (1982b, 2001b) was clearly not monophyletic. Latiff (2001b) transferred five species of Cissus to Nothocissus, but these new combinations (Latiff, 2001b) were questionable. Based on the sister phylogenetic relationships of the type species N. spicifera and Ampelocissus sect. Kalocissus (Fig. 1, Clade C) in this study as well as the similarity of their floral structure and seeds (extremely rugose) (Latiff, 1982b), we suggest N. spicifera need to be best transferred to Ampelocissus, whereas the other ‘‘Nothocissus” species likely form a new genus associated with Neotropical C. trianae according to their close phylogenetic relationship (Liu et al., 2013) or maintaining them as part of Cissus s.l. (J. Wen, unpublished data). Clade E consists of species of Ampelocissus sampled from Africa and a few taxa from tropical Asia, including the type species of Ampelocissus, A. latifolia (BS = 88%; PP = 1.00; Fig. 1). These taxa possess thyrsoid inflorescences with pedicellate flowers. Their seeds are oval, more or less compressed, rugose, flattened and with wide or linear ventral infolds, except for A. martini, which has relatively smooth seeds (Chen and Manchester, 2007). These taxa are 225 mainly distributed in dry and open areas in Africa and Southeast Asia, and correspond to Ampelocissus sect. Ampelocissus recognized by Planchon (1887) excluding the Central American species. We have not sampled the Australian Ampelocissus species, but they should be part of clade E based on the morphology of inflorescences and seeds (Planchon, 1887; Jackes, 1984; Chen and Manchester, 2007). 4.2. The New World origin of Vitis Our dating analyses suggest that the Ampelocissus–Vitis clade has its origin in the late Cretaceous (70.5 Ma, 95% HPD: 57.9– 82.0 Ma; node 1 in Fig. 2). Vitis is estimated to have split from its close relatives from Central America in the late Eocene (39.4 Ma, 95% HPD: 32.6–48.6 Ma; node 2, Fig. 2). The diversification of the Vitis crown group occurred in the late Eocene (37.3 Ma, 95% HPD: 30.9–45.1 Ma; node 3 in Fig. 2), with the differentiation of subg. Muscadinia from the New World and subg. Vitis from the Old and the New World. Our estimated divergence time of Vitis is earlier than that of Wan et al. (2013), which suggests the crown age of Vitis at 28.32 Ma. In subg. Vitis, the Eurasian lineage is estimated to have split from the New World clade at least at 35 ± 2.0 Ma (late Eocene) (Fig. 2), because Vitis glabra from the late Eocene of London Clay is the most reliable fossil record of an early member of subg. Vitis (Chandler, 1962). Our RASP and Lagrange analyses suggest that Vitis originated in the New World (nodes a and b in Fig. 3). Péros et al. (2011) suggested that subg. Vitis had its origin in Asia, and then dispersed to Europe and North America because the Asian chloroplast haplotypes were ancestral. However, their phylogenetic relationships within subg. Vitis were not well supported based on their consensus Bayesian tree of combined chloroplast data. Zecca et al. (2012) suggested that the North American species of Vitis were older than the Asian ones, however, their result was not conclusive. In their study, the divergence time of two the subgenera of Vitis in the early Miocene (from 18.60 to 19.05 Ma) was much later than the fossil record of subg. Vitis (Vitis glabra) from the London Clay in the late Eocene (Chandler, 1962). Wan et al. (2013) suggested that the Eurasian species were nested within the North American Vitis and the divergence of the Eurasian and North American taxa occurred at 11.12 Ma. This divergence time was also much later than the fossil record of the Eurasian Vitis (Vitis glabra) (Chandler, 1962). In the abovementioned studies, the sampling of non-Vitis taxa in Vitaceae was limited. Our study estimates that Vitis originated in the New World in the late Eocene, which is consistent with the fossil record. The seed fossil records show Vitis species were widely distributed from the Eocene to the Pliocene of the Tertiary in North America and Europe including western Siberia (Chandler, 1957, 1962, 1963, 1964; Tiffney and Barghoorn, 1976; Tiffney, 1979; Manchester, 1994; FaironDemaret and Smith, 2002; Manchester and McIntosh, 2007; Gong et al., 2010). The oldest confirmed fossil of the Ampelocissus–Vitis clade is Ampelocissus parvisemina, which dates back to the late Paleocene in western North America (Chen and Manchester, 2007). The fossil record of Vitis (for example, the fossil seeds of Vitis thunbergii from the Pliocene in Japan) in eastern Asia (Miki, 1956) is much younger, which seems to argue against the Vitis migration route from America to Asia and Europe of Wan et al. (2013). The fossil record is consistent with the biogeographic scenario that Vitis originated in the New World, then dispersed to Europe, and finally to Asia, i.e., the ‘‘Out of Americas” hypothesis (Miller et al., 2011). Recent studies showed that many plant lineages originated in the New World, with subsequent dispersal to the Old World (Davis et al., 2002, 2004; Jeandroz et al., 1997; Nie et al., 2006, 2012; Schultheis and Donoghue, 2004; Tu et al., 2010; Wen, 2011; Wen et al., 2010; Xie et al., 2009, 2010; Zhou et al., 2012). Nevertheless, eastern Asia has been suggested to be the ancestral area for many 226 X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 eastern Asian – eastern North American disjunct groups (Donoghue and Smith, 2004; Milne, 2006; Wen, 1999; Wen et al., 2010). Wan et al. (2008) suggested that a region in China might be one of the major centers of Vitis diversity in Asia with over 30 species. This region lies in the Qingling-Bashan Mountains and the provinces of Jiangxi, Hubei, Hunan, and Guangxi in China. The extinction rate of species was reported to be lower in Asia, higher in North America, and the highest in Europe among Northern Hemisphere continents (Donoghue et al., 2001; Péros et al., 2011; Ricklefs, 2005). The modern distribution pattern of Vitis with higher species richness in eastern Asia probably resulted from climatic fluctuations and paleogeographic changes during the late Tertiary and the Quaternary periods, which might have caused the range reduction and widespread extinction of Vitis members in the northern latitudes and pushed taxa southward (Aradhya et al., 2008). Detailed analyses of Vitis based on phylogenetic results and niche modeling (also see Wen et al., 2013b) might shed insights into the distributional dynamics of Vitis in the Tertiary and the Quaternary. Three major hypotheses have been proposed to explain the intercontinental vicariance/migrations between North America and Eurasia. The North Atlantic land bridges (NALB) across the north end of the Atlantic Ocean linking northern Canada to Europe via Greenland have been viewed as a principal route for the intercontinental spread of thermophilic boreotropical flora between the Old and the New Worlds in the early Tertiary (Davis et al., 2002, 2004; Fritsch and Cruz, 2012; Tiffney, 1985a,b; Tiffney and Manchester, 2001; Wen, 1999). NALB is speculated to have existed from the early Eocene until the late Miocene, although it was possibly interrupted during the Oligocene (Manchester, 1999). The most drastic cooling after the thermal maximum did not occur until the beginning of the Oligocene (Wolfe, 1975; Zachos et al., 2001). Boreotropical vegetation existed at much higher latitudes (50–60°N) and floristic exchanges might have occurred frequently between the Old and the New World in the Northern Hemisphere during that time (Tiffney and Manchester, 2001). In the current study, the Eurasian Vitis lineage is estimated to have split from that of the New World at least during the late Eocene (37.3 Ma, 95% HPD: 30.9–45.1 Ma; node 3 in Fig. 2). During the Eocene, many fossils of thermophilic taxa were recovered in the Northern Hemisphere (Reid and Chandler, 1933; Chandler, 1964; Wolfe, 1975; Tiffney, 1985b), which indicated that climates during that time could support the existence of thermophilic vegetation at high latitudes (Tiffney, 1985a,b). Based on the New World origin of Vitis as well as the Vitis fossil records older in Europe than those in Asia, we suggest that Vitis migrated from North America firstly to Europe, then to Asia. Although most modern species of Vitis are distributed in the temperate regions of the Northern Hemisphere, Vitis species are also extending to the Neotropics; for example, Vitis tiliifolia extends southward to Central America and the northern border of South America and V. popenoei is native to Central America. Vitis thus contains thermophilic elements of the boreotropical flora. The NALB might be the plausible migration route of Vitis from North America to Eurasia. Another possible migration route was the Bering land bridge (BLB), which connected northeastern Asia and northwestern North America (Emadzade et al., 2011; Riggins and Seigler, 2012; Tiffney and Manchester, 2001; Wen, 1999). BLB has been suggested to be open to terrestrial organisms from the early Paleocene until its closure between 7.4 and 4.8 Ma (Tiffney and Manchester, 2001). Donoghue and Smith (2004) favored BLB over NALB as the primary pathway between eastern Asia and the New World, because many temperate forest plant groups dispersed to the New World from the Old World mostly during the last 30 Ma (also see Wen et al., 2010). If Vitis migration was via BLB, the most parsimonious scenario might be that Vitis species migrated from North America to eastern Asia first, subsequently reaching Europe. Such scenario is inconsistent with the fossil records that European fossils are older than the eastern Asia ones (Chandler, 1962; Miki, 1956), which indicates that migration via BLB is less likely. A third possible explanation of the North American-Eurasian disjunction was intercontinental long distance dispersal (LDD). Although LDD is considered as an ad hoc explanation when a disjunct distribution cannot be explained by other factors (Erkens et al., 2009), it has been mainly viewed as a dominant mechanism of distribution of many very young plant groups (Lavin et al., 2004; Renner, 2004; Clayton et al., 2009; Bartish et al., 2011). If the Vitis migration was via LDD, the migration route might be that Vitis dispersed directly from eastern North America to western Europe, and subsequently reaching Asia. Although the dispersal of Vitis via LDD does not seem to a parsimonious scenario because the migration from North America to Europe needs to span the broad North Atlantic region, LDD cannot be eliminated as a likely mechanism. In conclusion, the fossil evidence combined with phylogenetic and dating results indicates that Vitis migration between the New and the Old Worlds was most likely via NALB or LDD. Acknowledgments We thank X.Z. Kan, Y. Meng, Deden Girmansyah and Y.M. Shui for collecting leaf material or laboratory assistance and also acknowledge support by the US National Science Foundation (DEB 0743474 to S.R. Manchester and J. Wen), the National Natural Science Foundation of China (Grant No. 31370249), the Smithsonian Endowment Grant Program, the Small Grant Program of the National Museum of Natural History of the Smithsonian Institution, and John D. and Catherine T. MacArthur Foundation, the Natural Science Foundation of Hubei Province of China (Grant No. 2013CFB199), and the Fundamental Research Funds for the Central Universities, China (Program No. 2011QC079). Appendix A. Supplementary material Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.ympev.2015.10. 013. References Anderssons, L., Rova, J.H.E., 1999. The rps16 intron and the phylogeny of the Rubioideae (Rubiaceae). Plant Syst. Evol. 214, 161–186. Aradhya, M., Koehmstedt, A., Prins, B.H., Dangl, G.S., Stover, E., 2008. Genetic structure, differentiation, and phylogeny of the genus Vitis: implications for genetic conservation. Acta Horticult. 799, 43–49. Bartish, I.V., Antonelli, A., Richardson, J.E., Swenson, U., 2011. Vicariance or longdistance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae). J. Biogeogr. 38, 177–190. Bell, C.D., Solits, D.E., Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. Amer. J. Bot. 97, 1296–1303. Brizicky, G.K., 1965. The genera of Vitaceae in the southeastern United States. J. Arnold Arbor. 46, 48–67. Chandler, M.E.J., 1957. The Oligocene flora of the Bovey Tracey lake basin, Devonshire. Bull. Brit. Mus. Nat. Hist. Geol. 3, 72–123. Chandler, M.E.J., 1960. Plant remains of the Hengistbury and Barton beds. Bull. Brit. Mus. Nat. Hist. Geol. 4, 191–238. Chandler, M.E.J., 1961. The Lower Tertiary Floras of Southern England. I. Palaeocene Floras. London Clay Flora (Supplement). British Museum (Natural History), London, UK, pp. 77–259. Chandler, M.E.J., 1962. The Lower Tertiary Floras of Southern England. II. Flora of the Pipe-Clay Series of Dorset (Lower Bagshot). British Museum (Natural History), London, UK, pp. 100–110. Chandler, M.E.J., 1963. The Lower Tertiary Floras of Southern England. III. Flora of the Bournemouth Beds; the Boscombe, and the Highcliff Sands. British Museum (Natural History), London, UK, pp. 101–103. Chandler, M.E.J., 1964. The Lower Tertiary Floras of Southern England. IV. A Summary and Survey of Findings in the Light of Recent Botanical Observations. British Museum (Natural History), London, UK, pp. 130–131. X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 Chen, I., 2009. History of Vitaceae inferred from morphology-based phylogeny and the fossil record of seeds (Ph.D. Dissertation). University of Florida, Gainesville, USA. Chen, I., Manchester, S.R., 2007. Seed morphology of modern and fossil Ampelocissus (Vitaceae) and implications for phytogeography. Am. J. Bot. 94, 1534–1553. Chen, I., Manchester, S.R., 2011. Seed morphology of Vitaceae. Int. J. Plant Sci. 172, 1–35. Chen, P.T., Chen, L.Q., Wen, J., 2011a. The first phylogenetic analysis of Tetrastigma (Miq.) Planch., the host of Rafflesiaceae. Taxon 60, 499–512. Chen, P.T., Wen, J., Chen, L.Q., 2011b. Spatial and temporal diversification of Tetrastigma (Vitaceae). Gard. Bull. Singapore 63, 307–327. Chen, Z.D., Ren, H., Wen, J., 2007. Vitaceae. In: Wu, C.Y., Hong, D.Y., Raven, P.H. (Eds.), Flora of China, vol. 12. Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, pp. 173–222. Clayton, J.W., Soltis, P.S., Soltis, D.E., 2009. Recent long-distance dispersal overshadows ancient biogeographical patterns in a pantropical angiosperm family (Simaroubaceae, Sapindales). Syst. Biol. 58, 395–410. Collinson, M.E., 1983. Fossil Plants of the London Clay. The Palaeontological Association, London, UK, pp. 98–99. Comeaux, B.L., Nesbitt, W.B., Fantz, P.R., 1987. Taxonomy of the native grapes of North Carolina. Castanea 52, 197–215. Davis, C.C., Bell, C.D., Mathews, S., Donoghue, M.J., 2002. Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proc. Natl. Acad. Sci. USA 99, 6833–6837. Davis, C.C., Fritsch, P.W., Bell, C.D., Mathews, S., 2004. High-latitude Tertiary migrations of an exclusively tropical clade: evidence from Malpighiaceae. Int. J. Plant Sci. 165 (suppl.), S107–S121. Di Gaspero, G., Peterlunger, E., Testolin, R., Edwards, K.J., Cipriani, G., 2000. Conservation of microsatellite loci within the genus Vitis. Theor. Appl. Genet. 101, 301–308. Donoghue, M.J., Bell, C.D., Li, J., 2001. Phylogenetic patterns in Northern Hemisphere plant geography. Int. J. Plant Sci. 162, S41–S52. Donoghue, M.J., Smith, S.A., 2004. Patterns in the assembly of temperate forests around the Northern Hemisphere. Philos. Trans. Roy. Soc. B (Biol. Sci.) 359, 1633–1644. Drummond, A.J., Ho, S.Y.W., Rawlence, N., Rambaut, A., 2007. A rough guide to BEAST 1.4. University of Auckland, Auckland, New Zealand. <http://code.google.com/p/beast-mcmc/downloads/list>. Drummond, A.J., Rambaut, A., 2007. BEAST: bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. Drummond, A.J., Ho, S.Y.W., Phillips, M.J., Rambaut, A., 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, 699–710. Edgar, R.C., 2004. MUSCLE, multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 32, 1792–1797. Emadzade, K., Gehrke, B., Linder, H.P., Hörandl, E., 2011. The biogeographical history of the cosmopolitan genus Ranunculus L. (Ranunculaceae) in the temperate to meridional zones. Mol. Phylogenet. Evol. 58, 4–21. Erkens, R.H.J., Maas, J.W., Couvreur, T.L.P., 2009. From Africa via Europe to South America: migrational route of a species-rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae). J. Biogeogr. 36, 2338–2352. Fairon-Demaret, M., Smith, T., 2002. Fruits and seeds from the Tienen Formation at Dormaal, Palaeocene–Eocene transition in eastern Belgium. Rev. Palaeobot. Palynol. 122, 47–62. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791. Fitch, W.M., 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416. Fritsch, P.W., Cruz, B.C., 2012. Phylogeny of Cercis based on DNA sequences of nuclear ITS and four plastid regions: implications for transatlantic historical biogeography. Mol. Phylogenet. Evol. 62, 816–825. Galet, P., 1967. Recherches sur les méthodes d’identification et de classification des Vitacées des zones tempérées (Ph.D. Thesis). Université de Montpellier, Montpellier, France. Galet, P., 1988. Cépages et vignobles de France. Tome 1. Lesvignes Américaines. Pierre Galet, Montpellier, France. Gerrath, J.M., Poluszny, U., 2007. Shoot architecture in the Vitaceae. Can. J. Bot. 85, 691–700. Gong, F., Karsai, I., Liu, Y.S., 2010. Vitis seeds (Vitaceae) from the late Neogene Gray fossil site, northeastern Tennessee, USA. Rev. Palaeobot. Palynol. 162, 71–83. Greguss, P., 1969. Tertiary Angiosperm Woods in Hungary. Akádemiai Kiádo, Budapest, Hungary, pp. 1–152. Herrera, F., Manchester, S.R., Jaramillo, C., 2012. Permineralized fruits from the late Eocene of Panama give clues of the composition of forests established early in the uplift of Central America. Rev. Palaeobot. Palynol. 175, 10–24. Huelsenbeck, J.P., Ronquist, F.R., 2001. MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755. Ickert-Bond, S.M., Gerrath, J.M., Wen, J., 2014. Gynoecium structure of Vitaceae and Leeaceae and implications for placentation evolution in the rosids. Intl. J. Plant Sci. 175, 998–1032. Ickert-Bond, S.M., Gerrath, J.M., Posluszny, U., Wen, J., 2015. Inflorescence development in the Vitis-Ampelocissus clade of Vitaceae: the lamellate inflorescence of Pterisanthes confirms the Ampelocissus Bauplan. Bot. J. Linn. Soc. 179, 725–741. Ingrouille, M.J., Chase, M.W., Fay, M.F., Bowman, D., Van der Bank, M., Bruijin, A.D.E., 2002. Systematics of Vitaceae from the viewpoint of plastid rbcL sequence data. Bot. J. Linn. Soc. 138, 421–432. 227 Jackes, B.R., 1984. Revision of the Australian Vitaceae. I. Ampelocissus Planchon. Austrobaileya 2, 81–86. Jeandroz, S., Roy, A., Bousquet, J., 1997. Phylogeny and phylogeography of the circumpolar genus Fraxinus (Oleaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA. Mol. Phylogenet. Evol. 7, 241–251. Latiff, A., 1982a. Studies in Malesian Vitaceae IV. The genera Ampelocissus, Ampelopsis and Parthenocissus in the Malay Peninsula. Fed. Mus. J. 27, 78–93. Latiff, A., 1982b. Studies in Malesian Vitaceae II. Nothocissus: a new Malesian genus. Fed. Mus. J. 27, 70–75. Latiff, A., 1982c. Studies in Malesian Vitaceae I. A revision of Pterisanthes Bl. Fed. Mus. J. 27, 42–69. Latiff, A., 1982d. Studies in Malesian Vitaceae III. Ampelocissus complanata, a new species from Borneo. Fed. Mus. J. 27, 75–77. Latiff, A., 2001a. Studies in Malesian Vitaceae XII: taxonomic notes on Cissus, Ampelocissus, Nothocissus and Tetrastigma and other genera. Folia Malays. 2, 179–189. Latiff, A., 2001b. Diversity of the Vitaceae in the Malay Archipelago. Malay Nat. J. 55, 29–42. Lavin, M., Schrire, B.P., Lewis, G., Pennington, R.T., Delgado-Salinas, A., Thulin, M., Hughes, C.E., Matos, A.B., Wojciechowski, M.F., 2004. Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philos. Trans. Roy. Soc. B (Biol. Sci.) 359, 1509–1522. Lee, C., Wen, J., 2004. Phylogeny of Panax using chloroplast trnC–trnD intergenic region and the utility of trnC–trnD in interspecific studies of plants. Mol. Phylogenet. Evol. 31, 894–903. Liu, X.Q., Ickert-Bond, S.M., Chen, L.Q., Wen, J., 2013. Molecular phylogeny of Cissus L. of Vitaceae (the grape family) and evolution of its pantropical intercontinental disjunctions. Mol. Phylogenet. Evol. 66, 43–53. Lombardi, J.A., 1997. Types of names in Ampelopsis and Cissus (Vitaceae) referring to taxa in the Caribbean, Central N. America. Taxon 46, 423–432. Lombardi, J.A., 1999. A new combination in Ampelocissus (Vitaceae), a victim of historic deforestation in Nicaragua. Novon 9, 423–424. Lombardi, J.A., 2000. Vitaceae—gêneros Ampelocissus, Ampelopsis e Cissus. Flora Neotrop. Monogr. 80, 1–250. Lombardi, J.A., 2005. Three new species of Vitaceae from Mesoamerica. Novon 15, 562–567. Lu, L., Wang, W., Chen, Z., Wen, J., 2013. Phylogeny of the non-monophyletic Cayratia Juss. (Vitaceae) and implications for character evolution and biogeography. Mol. Phylogenet. Evol. 68, 502–515. Magallón, S.A., Castillo, A., 2009. Angiosperm diversification through time. Am. J. Bot. 96, 349–365. Mai, D.H., 2000. The Lower Miocene floras of the Spremberger sequence and the second brown coal horizon in the Lusatica region. Part III: dialypetalae and sympetalae. Palaeontogr. Abt. B 253, 1–106. Manchester, S.R., 1994. Fruits and seeds of the middle Eocene nut beds flora, Clarno Formation, Oregon. Palaeontogr. Am. 58, 1–114. Manchester, S.R., 1999. Biogeographical relationships of North American Tertiary floras. Ann. Mo. Bot. Gard. 86, 472–522. Manchester, S.R., Kapgate, D.K., Wen, J., 2013. Oldest fruits of the grape family (Vitaceae) from the Late Cretaceous Deccan Cherts of India. Am. J. Bot. 100, 1849–1859. Manchester, S.R., McIntosh, W., 2007. Late Eocene silicified and seeds from the John Day Formation near Post, Oregen. PaleoBios 27, 1–17. Mau, B., Newton, M., Larget, B., 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55, 1–12. Miki, S., 1956. Seed remains of Vitaceae in Japan. J. Inst. Polytech. Osaka City Univ. Ser. D 7, 247–271. Miller, A.J., Matasci, N., Schwaninger, H., Aradhya, M.K., Prins, B., Zhong, G.Y., Simon, C., Buckler, E.S., Myles, S., 2014. Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS ONE 8 (11), e78680. http://dx. doi.org/10.1371/journal.pone.0078680. Miller, J.S., Kamath, A., Damashek, J., Levin, R.A., 2011. Out of America to Africa or Asia: inference of dispersal histories using nuclear and plastid DNA and the SRNase self-incompatibility locus. Mol. Biol. Evol. 28, 793–801. Milne, R.I., 2006. Northern hemisphere plant disjunctions: a window on Tertiary land bridges and climate change? Ann. Bot. 98, 465–472. Moore, M.O., 1991. Classification and systematics of eastern North American Vitis L. (Vitaceae) north of Mexico. SIDA 14, 339–367. Moore, M.O., Wen, J., in press. Vitaceae. In: Flora of North America Editorial Committee (Ed.), Flora of North America, North of Mexico, vol. 12. Oxford University Press, New York and Oxford (in press). Müller, K., 2005. SeqState—primer design and sequence statistics for phylogenetic DNA data sets. Appl. Bioinform. 4, 65–69. Nie, Z.L., Sun, H., Beardsley, P.M., Olmstead, R.G., Wen, J., 2006. Evolution of biogeographic disjunction between eastern Asia and eastern North America in Phryma (Phrymaceae). Am. J. Bot. 93, 1343–1356. Nie, Z.L., Sun, H., Chen, Z.D., Meng, Y., Manchester, S.R., Wen, J., 2010. Molecular phylogeny and biogeographic diversification of Parthenocissus (Vitaceae) disjunct between Asia and North America. Am. J. Bot. 97, 1342–1353. Nie, Z.L., Sun, H., Manchester, S.R., Meng, Y., Luke, Q., Wen, J., 2012. Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae). BMC Evol. Biol. 12, 17. http://dx.doi.org/10.1186/14712148-12-17. Nylander, J.A.A., 2004. MrModeltest, version 2 (computer program). Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. 228 X.-Q. Liu et al. / Molecular Phylogenetics and Evolution 95 (2016) 217–228 Oxelman, B., Liden, M., Berglund, D., 1997. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Syst. Evol. 206, 393–410. Paleobiological Database. 2010. <http://paleodb.org/cgi-bin/bridge.pl>. Pelsy, F., 2007. Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus Vitis. Theor. Appl. Genet. 116, 15–27. Péros, J.P., Berger, G., Portemont, A., Boursiquot, J.-M., Lacombe, T., 2011. Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae). J. Biogeogr. 38, 471–486. Planchon, J.E., 1887. Monographie des Ampélidées vrais. In: De Candolle, A.F.P.P., De Candolle, C. (Eds.), Monographiae Phanaerogamarum 5(2). Sumptibus G. Masson, Paris, pp. 305–654. Rambaut, A., 2002. Se-Al: sequence alignment editor, version 2.0 a11 Oxford: University of Oxford. <http://tree.bio.ed.ac.uk/software/seal/> Rannala, B., Yang, Z.H., 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304–311. Ree, R.H., Smith, S.A., 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst. Biol. 57, 4–14. Reid, E.M., Chandler, M.E.J., 1933. The London Clay. British Museum (Natural History), London, UK. Ren, H., Lu, L.M., Soejima, A., Luke, Q., Zhang, D.X., Chen, Z.D., Wen, J., 2011. Phylogenetic analysis of the grape family (Vitaceae) based on the noncoding plastid trnC-petN, trnH-psbA, and trnL-F sequences. Taxon 60, 629–637. Renner, S.S., 2004. Multiple miocene melastomataceae dispersal between Madagascar, Africa and India. Philos. Trans. Roy. Soc. B (Biol. Sci.) 359, 1485– 1494. Ricklefs, R.E., 2005. Historical and ecological dimensions of global patterns in plant diversity. Biol. Skrifter (Roy. Dan. Acad. Sci. Lett.) 55, 583–603. Riggins, C.W., Seigler, D.S., 2012. The genus Artemisia (Asteraceae: Anthemideae) at a continental crossroads: Molecular insights into migrations, disjunctions, and reticulations among Old and New World species from a Beringian perspective. Mol. Phylogenet. Evol. 64, 471–490. Rodrigues, J.G., Lombardi, J.A., Lovato, M.B., 2014. Phylogeny of Cissus (Vitaceae) focusing on South American species. Taxon 63, 287–298. Ronquist, F., 1997. Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst. Biol. 46, 195–203. Rossetto, M., Crayn, D.M., Jackes, B.R., Porter, C., 2007. An updated estimate of intergeneric phylogenetic relationships in the Australian Vitaceae. Can. J. Bot. 85, 722–730. Rossetto, M., Jackes, B.R., Scott, K.D., Henry, R.J., 2002. Is the genus Cissus (Vitaceae) monophyletic? Evidence from plastid and nuclear ribosomal DNA. Syst. Bot. 7, 522–533. Schultheis, L.M., Donoghue, M.J., 2004. Molecular phylogeny and biogeography of Ribes (Grossulariaceae), with an emphasis on gooseberries (subg. Grossularia). Syst. Bot. 29, 77–96. Seemann, B., 1869. Description of two new species of Vitis from Central America. J. Bot. 7, 332–333. Simmons, M.P., Ochoterena, H., 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49, 36–381. Soejima, A., Wen, J., 2006. Phylogenetic analysis of the grape family (Vitaceae) based on three chloroplast markers. Am. J. Bot. 93, 278–287. Stein, D.B., Palmer, J.D., Thompson, W.F., 1986. Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda. Curr. Genet. 10, 835–841. van Steenis, C.G.G.J., Bakhuizen van Den Brink, R.G., 1967. Miscellaneous botanical notes XVI. 104: two new Bornean Pterisanthes (Vitaceae). Engl. Bot. Jahrb. 86, 385–390. Süssenguth, K., 1953. Vitaceae. In: Engler, A., Prantl, K. (Eds.), Die Natürlichen Pflanzenfamilien, vol. 20. Duncker & Humblot, Berlin, pp. 174–333. Swofford, D.L., 2003. PAUP⁄: phylogenetic analysis using parsimony (⁄ and other methods), version 4.0b10. Sinauer, Sunderland, Massachusetts. Taberlet, P., Gielly, L., Pautou, G., Bouvet, J., 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17, 1105–1109. Thiv, M., van der Niet, T., Rutschmann, F., Thulin, M., Brune, T., Linder, H.P., 2011. Old-New World and trans-African disjunctions of Thamnosma (Rutaceae): intercontinental long-distance dispersal and local differentiation in the succulent biome. Am. J. Bot. 98, 76–87. Thorne, J.L., Kishino, H., 2002. Divergence time estimation and rate evolution with multilocus data sets. Syst. Biol. 51, 689–702. Thorne, J.L., Kishino, H., Painter, I.S., 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647–1657. Tiffney, B.H., 1979. Nomenclatural revision: Brandon Vitaceae. Rev. Palaeobot. Palynol. 27, 91–92. Tiffney, B.H., 1985a. Perspectives on the origin of the floristic similarity between eastern Asia and eastern North America. J. Arnold Arbor. 66, 73–94. Tiffney, B.H., 1985b. The Eocene North Atlantic land bridge: its importance in Tertiary and modern phytogeography of the northern hemisphere. J. Arnold Arbor. 66, 243–273. Tiffney, B.H., 1994. Re-evaluation of the age of the Brandon Lignite (Vermont, USA) based on plant megafossils. Rev. Palaeobot. Palynol. 82, 299–315. Tiffney, B.H., Barghoorn, E.S., 1976. Fruits and seeds of Brandon Lignite. I. Vitaceae. Rev. Palaeobot. Palynol. 22, 169–191. Tiffney, B.H., Manchester, S.R., 2001. The use of geological and paleontological evidence in evaluating plant phylogeographic hypotheses in the Northern Hemisphere Tertiary. Int. J. Plant Sci. 162 (suppl.), S3–S17. Trias-Blasi, A., Parnell, J.A.N., Hodkinson, T.R., 2012. Multi-gene region phylogenetic analysis of the grape family (Vitaceae). Syst. Bot. 37, 941–950. Tröndle, D., Schröder, S., Kassemeyer, H.H., Kiefer, C., Koch, M.A., Nick, P., 2010. Molecular phylogeny of the genus Vitis (Vitaceae) based on plastid markers. Am. J. Bot. 97, 1168–1178. Tu, T.Y., Volis, S., Dillon, M.O., Sun, H., Wen, J., 2010. Dispersals of Hyoscyanmeae and Mandrangoreae (Solanaceae) from the New World to Eurasia in the early Miocene and their biogeographic diversification within Eurasia. Mol. Phylogenet. Evol. 57, 1226–1237. Wan, Y., Schwaninger, H., Baldo, A.M., Labate, J.A., Zhong, G.Y., Simon, C.J., 2013. A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during Neogene and Quaternary climate change. BMC Evol. Biol. 13, 141. http://dx.doi.org/10.1186/1471-2148-13-141. Wan, Y., Schwaninger, H., Simon, C.J., Wang, Y., He, P., 2008. The eco-geographic distribution of wild grape germplasm in China. Vitis 47, 77–80. Wen, J., 1999. Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Ann. Rev. Ecol. Syst. 30, 421–455. Wen, J., 2007. Vitaceae. In: Kubitzki, K. (Ed.), The Families and Genera of Vascular Plants, vol. 9. Springer-Verlag, Berlin, pp. 466–478. Wen, J., 2011. Systematics and biogeography of Aralia L. (Araliaceae): revision of Aralia sects. Aralia, Humiles, Nanae, and Sciadodendron. Contr. United States Nat. Herb. 57, 1–172. Wen, J., Boggan, J.K., Nie, Z.L., 2014. Synopsis of Nekemias Raf., a segregate genus from Ampelopsis Michx. (Vitaceae) disjunct between eastern/southeastern Asia and eastern North America, with ten new combinations. PhytoKeys 42, 11–19. Wen, J., Ickert-Bond, S.M., Nie, Z.L., Li, R., 2010. Timing and modes of evolution of eastern Asian – North American biogeographic disjunctions in seed plants. In: Long, M., Gu, H., Zhou, Z. (Eds.), Darwin’s Heritage Today: Proceedings of the Darwin 200 Beijing International Conference. Higher Education Press, Beijing, pp. 252–269. Wen, J., Lu, L.M., Boggan, J.K., 2013a. Diversity and evolution of Vitaceae in the Philippines. Philipp. J. Sci 142 (Special Issue), 223–244. Wen, J., Nie, Z.L., Soejima, A., Meng, Y., 2007. Phylogeny of Vitaceae based on the nuclear GAI1 gene sequences. Can. J. Bot. 85, 731–745. Wen, J., Ree, R.H., Ickert-Bond, S., Nie, Z.L., Funk, V., 2013b. Biogeography: where do we go from here? Taxon 62, 912–927. Wen, J., Xiong, Z.Q., Nie, Z.L., Mao, L.K., Zhu, Y.B., Kan, X.Z., Ickert-Bond, S.M., Gerrath, J., Zimmer, E.A., Fang, X.D., 2013c. Transcriptome sequences resolve deep relationships of the grape family. PLoS ONE 8, e74394. http://dx.doi.org/ 10.1371/journal.pone.0074394. Wen, J., Zimmer, E.A., 1996. Phylogeny of Panax L. (the ginseng genus, Araliaceae): inferences from ITS sequences of nuclear ribosomal DNA. Mol. Phylogenet. Evol. 6, 167–179. Wheeler, E.A., Lapasha, C.A., 1994. Woods of the Vitaceae–fossil and modern. Rev. Palaeobot. Palynol. 80, 175–207. White, T.J., Bruns, T., Lee, S., Taylor, J., 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M., Gelfand, D., Sninsky, J., White, T. (Eds.), PCR Protocols: A Guide to Methods and Application. Academic Press, San Diego, pp. 315–322. Wikström, N., Savolainen, V., Chase, M.W., 2001. Evolution of the angiosperms: calibrating the family tree. Proc. Roy. Soc. Lond. B 268, 2211–2220. Wilson, T., Posluszny, U., 2003. Complex tendril branching in two species of Parthenocissus: implications for the vitaceous shoot architecture. Can. J. Bot. 81, 587–597. Wolfe, J.A., 1975. Some aspects of plant geography of the Northern Hemisphere during the late Cretaceous and Tertiary. Ann. Mo. Bot. Gard. 62, 264–279. Xie, L., Wagner, W.L., Ree, R.H., Berry, P.E., Wen, J., 2009. Molecular phylogeny, divergence time estimates, and historical biogeography of Circaea (Onagraceae) in the Northern Hemisphere. Mol. Phylogenet. Evol. 53, 995–1009. Xie, L., Yi, T.S., Li, R., Li, D.Z., Wen, J., 2010. Evolution and biogeographic diversification of the witch-hazel genus (Hamamelis L., Hamamelidaceae) in the Northern Hemisphere. Mol. Phylogenet. Evol. 56, 675–689. Yu, Y., Harris, A.J., He, X., 2010. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Mol. Phylogenet. Evol. 56, 848–850. Zachos, J., Pagani, M., Sloan, L., Thomas, E., Billups, K., 2001. Trends, rhythms, and aberration in global climate 65 Ma to present. Science 292, 686–693. Zecca, G., Abbott, J.R., Sun, W.B., Spada, A., Sala, F., Grassi, F., 2012. The timing and the mode of evolution of wild grapes (Vitis). Mol. Phylogenet. Evol. 62, 736–747. Zhang, N., Wen, J., Zimmer, E.A., 2015. Expression patterns of AP1, FUL, FT and LEAFY orthologs in Vitaceae support the homology of tendrils and inflorescences throughout the grape family. J. Syst. Evol. 53, 469–476. http:// dx.doi.org/10.1111/jse.12138. Zhou, Z., Wen, J., Li, G., Sun, H., 2012. Phylogenetic assessment and biogeographic analyses of tribe Peracarpeae (Campanulaceae). Plant Syst. Evol. 298, 323–336. http://dx.doi.org/10.1007/s00606-011-0547-7.

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Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus.

Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus.

Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus.

Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus.

Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus.

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