Jun Wen

Publications of Jun Wen

• Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae).

  Authors: Ze-Long Nie, Hang Sun, Steven R Manchester, Ying Meng, Quentin Luke, Jun Wen

  BMC evolutionary biology. 02/2012; 12:17.

  ABSTRACT: The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, andABSTRACT: The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents. The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4 - 61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9 - 45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7 - 22.3 Ma). The global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants.

• Biogeographic disjunction between eastern Asia and North America in the Adiantum pedatum complex (Pteridaceae).

  Authors: Jin-Mei Lu, De-Zhu Li, Sue Lutz, Akiko Soejima, Tingshuang Yi, Jun Wen

  American journal of botany. 09/2011; 98(10):1680-93.

  • Premise of the study: Biogeographic analyses of ferns with an eastern Asian-North American disjunction are few. The Adiantum pedatum complex has such a disjunct distribution. The monophyly of the• Premise of the study: Biogeographic analyses of ferns with an eastern Asian-North American disjunction are few. The Adiantum pedatum complex has such a disjunct distribution. The monophyly of the complex needs to be tested and diversification history of the four species needs to be reconstructed. • Methods: Plastid (atpA, atpB, rbcL, trnL-F, and rps4-trnS) sequences of 100 accessions representing the biogeographic diversity of Adiantum were analyzed with parsimony and Bayesian inference. Biogeography of the Adiantum pedatum complex was inferred using programs DIVA and LAGRANGE. Divergence times of clades were estimated with the program BEAST. • Key results: The A. pedatum complex is monophyletic and sister to the eastern Asian A. edentulum. Accessions of A. pedatum do not form a clade; instead three subgroups are recognizable. The clade of A. aleuticum and A. viridimontanum is nested within A. pedatum. The Asian A. myriosorum is sister to the A. pedatum-A. aleuticum clade. Both DIVA and LAGRANGE analyses suggest an eastern Asian origin of the A. pedatum complex. The age of the crown A. pedatum complex is dated to be at 4.27 (2.24-6.57) million years ago. • Conclusions: The currently recognized eastern Asian-North American disjunct species A. pedatum needs to be segregated into three species, corresponding to populations in eastern North America, China, and Japan. The eastern Asian-North American disjunction in the complex is inferred to be the result of two intercontinental migrations, one from eastern Asia into North America in the late Tertiary and the other from North America back to eastern Asia in the Pleistocene.

• Phylogenetic relationships of Chinese Adiantum based on five plastid markers.

  Authors: Jin-Mei Lu, Jun Wen, Sue Lutz, Yi-Ping Wang, De-Zhu Li

  Journal of plant research. 08/2011; 125(2):237-49.

  Adiantum consists of about 150-200 species mostly with a pantropical distribution, yet the classifications of Adiantum have been based primarily on regional studies. Confounding the clarity ofAdiantum consists of about 150-200 species mostly with a pantropical distribution, yet the classifications of Adiantum have been based primarily on regional studies. Confounding the clarity of reconstructing the evolutionary history of Adiantum is that previous molecular phylogenetic studies suggest that a separate and distinctive clade, the vittarioids, may be derived from within Adiantum. Five plastid markers (atpA, atpB, rbcL, trnL-F and rps4-trnS) are employed to assess the monophyly of Adiantum, and construct the molecular phylogeny of Chinese Adiantum. Our analyses support the monophyly of Adiantum. All temperate Adiantum species form a clade nested within the pantropical grade, suggesting a tropical origin of Adiantum. Six main clades are supported within Chinese Adiantum, which are only partially consistent with Lin's classification of the genus. Series Caudata is polyphyletic with series Gravesiana nested within one subgroup of series Caudata. The prolonged whip-like stolon at the apex of the fronds is the defining character for series Caudata, but it may have evolved multiple times. Adiantum reniforme with the simple fronds is sister to series Venusta, which has a decompound lamina with many flabellate to cuneate segments. Series Veneri-capilliformia is not monophyletic, with A. capillus-veneris sister to series Flabellulata except for A. diaphanum, and A. edentulum sister to series Pedata. Series Flabellulata is biphyletic with A. diaphanum nested within the pantropical grade. The phylogeny suggests that convergent evolution in frond architecture has occurred in Adiantum.

• DNA barcoding of Panax species.

  Authors: Yunjuan Zuo, Zhongjian Chen, Katsuhiko Kondo, Tsuneo Funamoto, Jun Wen, Shiliang Zhou

  Planta medica. 01/2011; 77(2):182-7.

  Ginsengs (Panax, Araliaceae) are among the plants best known for their medicinal properties. Many ginseng species are endangered due to over-exploitation of natural resources - a situation difficultGinsengs (Panax, Araliaceae) are among the plants best known for their medicinal properties. Many ginseng species are endangered due to over-exploitation of natural resources - a situation difficult to remedy while there are no reliable, practical methods for species identification. We screened eleven candidate DNA barcoding loci to establish an accurate and effective Panax species identification system, both for commercial and conservation purposes. We used 95 ginseng samples, representing all the species in the genus. We found considerable differences in the performance of the potential barcoding regions. The sequencing of ATPF-ATPH was unsuccessful due to poly-N structures. The RBCL, RPOB, and RPOC1 regions were found to be mostly invariable, with only four to eight variable sites. Using MATK, PSBK-I, PSBM-TRND, RPS16 and NAD1, we could identify four to six out of eight considerably divergent species but only one to five out of nineteen clusters within the P. bipinnatifidus species group. PSBA-TRNH and ITS were the most variable loci, working very well both in species and cluster identifications. We demonstrated that the combination of PSBA-TRNH and ITS is sufficient for identifying all the species and clusters in the genus.

• Dispersals of Hyoscyameae and Mandragoreae (Solanaceae) from the New World to Eurasia in the early Miocene and their biogeographic diversification within Eurasia.

  Authors: Tieyao Tu, Sergei Volis, Michael O Dillon, Hang Sun, Jun Wen

  Molecular phylogenetics and evolution. 12/2010; 57(3):1226-37.

  The cosmopolitan Solanaceae contains 21 tribes and has the greatest diversity in South America. Hyoscyameae and Mandragoreae are the only tribes of this family distributed exclusively in Eurasia withThe cosmopolitan Solanaceae contains 21 tribes and has the greatest diversity in South America. Hyoscyameae and Mandragoreae are the only tribes of this family distributed exclusively in Eurasia with two centers of diversity: the Mediterranean-Turanian (MT) region and the Tibetan Plateau (TP). In this study, we examined the origins and biogeographical diversifications of the two tribes based on the phylogenetic framework and chronogram inferred from a combined data set of six plastid DNA regions (the atpB gene, the ndhF gene, the rps16-trnK intergenic spacer, the rbcL gene, the trnC-psbM region and the psbA-trnH intergenic spacer) with two fossil calibration points. Our data suggest that Hyoscyameae and Mandragoreae each forms a monophyletic group independently derived from different New World lineages in the early Miocene. Phylogenetic relationships within both tribes are generally well resolved. All genera of Hyoscyameae are found to be monophyletic and they diversified in middle to late Miocene. At nearly the same time, Mandragoreae split into two clades, corresponding to the MT region and the TP region, respectively. Both the phylogenetic relationships and the estimated ages of Hyoscyameae and Mandragoreae support two independent dispersal events of their ancestors from the New World into Eurasia. After their arrivals in Eurasia, the two tribes diversified primarily in the MT region and in the TP region via multiple biogeographic processes including vicariance, dispersal, recolonization or being preserved as relicts, from the mid Miocene to the late Quaternary.

• Molecular phylogeny and biogeographic diversification of Parthenocissus (Vitaceae) disjunct between Asia and North America.

  Authors: Ze-Long Nie, Hang Sun, Zhi-Duan Chen, Ying Meng, Steven R Manchester, Jun Wen

  American journal of botany. 08/2010; 97(8):1342-53.

  • Premise of the study: Parthenocissus is a genus of the grape family Vitaceae and has a disjunct distribution in Asia and North America with members in both tropical and temperate regions. The• Premise of the study: Parthenocissus is a genus of the grape family Vitaceae and has a disjunct distribution in Asia and North America with members in both tropical and temperate regions. The monophyly of Parthenocissus has not yet been tested, and the species relationships and the evolution of its intercontinental disjunction have not been investigated with extensive sampling and molecular phylogenetic methods. • Methods: Plastid (trnL-F, rps16, and atpB-rbcL) and nuclear GAI1 sequences of 56 accessions representing all 12 Parthenocissus species were analyzed with parsimony, likelihood, and Bayesian inference. Divergence times of disjunct lineages were estimated with relaxed Bayesian dating. Evolution of the leaflet number was assessed by tracing this character onto Bayesian trees using the Trace Character Over Trees option in the program Mesquite. • Key results: Parthenocissus is monophyletic and sister to the newly described segregate genus Yua. Two major clades within Parthenocissus are recognizable corresponding to their distribution in Asia and North America. The disjunction between the two continents is estimated to be at 21.64 (95% higher posterior densities 10.23-34.89) million years ago. • Conclusions: Parthenocissus is likely to have derived from the Eocene boreotropical element. Its current Asian-North American disjunction is dated to the early Miocene, congruent with fossil and paleoclimatic evidence. The tropical species is nested within the temperate clade and is inferred to have dispersed from the adjacent temperate regions. Parthenocissus and Yua are best treated as distinct genera. Leaflet number in this genus has a complex history and cannot be used as a character for infrageneric classification.

• Genetic variation and conservation assessment of Chinese populations of Magnolia cathcartii (Magnoliaceae), a rare evergreen tree from the South-Central China hotspot in the Eastern Himalayas.

  Authors: Xue-Mei Zhang, Jun Wen, Zhi-Ling Dao, Timothy J Motley, Chun-Lin Long

  Journal of plant research. 05/2010; 123(3):321-31.

  Nine natural populations of the rare evergreen tree Magnolia cathcartii (Magnoliaceae) were sampled across its natural range, and amplified fragment length polymorphism (AFLP) markers were used toNine natural populations of the rare evergreen tree Magnolia cathcartii (Magnoliaceae) were sampled across its natural range, and amplified fragment length polymorphism (AFLP) markers were used to assess genetic variation within and among populations. Three ex situ populations were also surveyed to determine whether conservation plantings include the entire genetic diversity of the species. Genetic diversity within the natural populations was very low (0.122 for Nei's gene diversity), and the southeast populations had the highest diversity. The ex situ populations had a lower diversity than the mean diversity for all populations, and none of the ex situ populations reached the levels of diversity found in their source populations. Genetic differentiation was high among natural populations (G st = 0.247), and an isolation-by-distance pattern was detected. Habitat fragmentation, restricted gene flow, and geitonogamy are proposed to be the primary reasons for the low genetic diversity and high genetic differentiation. More protection is needed, especially for the southeast populations, which possess the highest numbers of unique alleles according to AFLP fragment analyses. The ex situ program was a good first step towards preserving this species, but the current ex situ populations preserve only a limited portion of its genetic diversity. Future ex situ efforts should focus on enhancing the plantings with individuals from southeastern Yunnan.

• Evolution and biogeographic diversification of the witch-hazel genus (Hamamelis L., Hamamelidaceae) in the Northern Hemisphere.

  Authors: Lei Xie, Ting-Shuang Yi, Rong Li, De-Zhu Li, Jun Wen

  Molecular phylogenetics and evolution. 02/2010; 56(2):675-89.

  The evolution of the eastern Asian and eastern North American disjunction of the witch-hazel genus Hamamelis L. (Hamamelidaceae) was examined through phylogenetic and biogeographic analyses.The evolution of the eastern Asian and eastern North American disjunction of the witch-hazel genus Hamamelis L. (Hamamelidaceae) was examined through phylogenetic and biogeographic analyses. Phylogenetic relationships of all Hamamelis species were reconstructed using parsimony and Bayesian analyses of sequence data from six plastid (trnL-F, psaA-ycf3, rps16, matK, atpB-rbcL, and psbA-trnH) and two nuclear (ITS and ETS) DNA regions. The phylogeny was then used to infer the biogeographic origin and subsequent diversification using both event-based (DIVA) and maximum likelihood (LAGRANGE) methods incorporating fossil data. The times of divergence within Hamamelis were estimated with the Bayesian approach using the program BEAST. A very low level of molecular variation was detected in both the plastid and the nuclear DNA regions within Hamamelis. The combined analyses resulted in a phylogeny of the genus with higher resolution and support values. Hamamelis was supported to be monophyletic with H. mollis from eastern China diverged first in the genus. All North American species formed a clade and was sister to the eastern Asian H. japonica. Within the North American clade, H. mexicana was sister to H. vernalis, and the recently described species H. ovalis was found to be closely related to the widespread species H. virginiana. The stem age of Hamamelis was estimated to be at the Eocene (51.2 mya, with 95% HDP: 49.0-54.6 mya), and the crown age of the genus was dated to be at the late Miocene (9.7 mya, with 95% HDP: 3.6-18.1 mya, or 10.6 mya, with 95% HDP: 4.2-19.6 mya). The disjunction between the eastern Asian and the eastern North American species was dated to be 7.1 mya (95% HDP: 3.1-13.6 mya) or 7.7 mya (95% HDP: 3.4-13.6 mya). Biogeographic analyses incorporating fossils resulted in more equally possible solutions at the stem lineage of Hamamelis than those including extant species only. Eastern Asia is inferred to be the most-likely area for the origin of Hamamelis. The current disjunction was due to the extinction in western North America and Europe from Eocene to late Miocene, and later migration from eastern Asia into North America. The Bering land bridge was hypothesized to have played an important role in the evolution of this disjunction. The current species diversity of the genus was the result of relatively recent diversification events during the late Miocene rather than long accumulation of lineages from the early Tertiary.

• Phylogeny and biogeography of the eastern Asian - North American disjunct wild-rice genus (Zizania L., Poaceae).

  Authors: Xinwei Xu, Christina Walters, Michael F Antolin, Mara L Alexander, Sue Lutz, Song Ge, Jun Wen

  Molecular phylogenetics and evolution. 11/2009;

  The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z.The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny of Zizania was constructed using sequences of seven DNA fragments (atpB-rbcL, matK, rps16, trnL-F, trnH-psbA, nad1, and Adh1a) from chloroplast, mitochondrial, and nuclear genomes. Zizania is shown to be monophyletic with the North American species forming a clade and the eastern Asian Z. latifolia sister to the North American clade. The divergence between the eastern Asian Z. latifolia and the North American clade was dated to be 3.74 (95% HPD: 1.04-7.23) million years ago (mya) using the Bayesian dating method with the combined atpB-rbcL, matK, rps16, trnL-F and nad1 data. Biogeographic analyses using a likelihood method suggest the North American origin of Zizania and its migration into eastern Asia via the Bering land bridge. Among the three North American species, the organellar data and the haplotype network of the nuclear Adh1a gene show a close relationship between Z. palustris and the narrowly distributed endangered species Z. texana. Bayesian dating estimated the divergence of North American Zizania to be 0.71 (95% HPD: 0.12-1.54) mya in the Pleistocene. The non-monophyly of Z. palustris and Z. aquatica in the organellar and nuclear data is most likely caused by incomplete lineage sorting, yet low-frequency unidirectional introgression of Z. palustris into Z. aquatica is present in the nuclear data as well.

• Development of microsatellite markers for the bracken fern, Pteridium aquilinum.

  Authors: Xiaoqing Chen, Jianxiu Wang, Hongli Tian, Xianchun Zhang, Jun Wen, Shiliang Zhou

  Molecular ecology resources. 11/2008; 8(6):1491-3.

  We isolated eight novel polymorphic microsatellite loci from Pteridium aquilinum. These loci were characterized in 30 individuals, one from Bolivia, two from Peru, one from the USA, one from Japan,We isolated eight novel polymorphic microsatellite loci from Pteridium aquilinum. These loci were characterized in 30 individuals, one from Bolivia, two from Peru, one from the USA, one from Japan, and 25 from Northeast China to Southwest China. The number of alleles per locus ranged from two to seven. The observed heterozygosity (H(O) ) ranged from 0.000 to 0.600 with an average of 0.3051, and the expected heterozygosity (H(E) ) ranged from 0.0966 to 0.7780 with an average of 0.4267. One locus deviated from Hardy-Weinberg equilibrium and four pairs of loci were found to be in linkage disequilibrium. These polymorphic loci will be useful in the study of the population genetic structure of Pteridium.

• Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications.

  Authors: Zhumei Ren, Bin Zhu, Enbo Ma, Jun Wen, Tieyao Tu, Ying Cao, Masami Hasegawa, Yang Zhong

  Gene. 10/2008;

  The complete nucleotide sequence of the mitochondrial (mt) genome of the crab-eating frog, Fejervarya cancrivora Gravenhorst (Amphibia: Anura: Ranidae), was determined. The mt genome is 17,843 bpThe complete nucleotide sequence of the mitochondrial (mt) genome of the crab-eating frog, Fejervarya cancrivora Gravenhorst (Amphibia: Anura: Ranidae), was determined. The mt genome is 17,843 bp long and contains 13 protein-coding (ATP6, ATP8, COI-III, ND1-6 and 4L, and Cyt b) and two ribosomal RNA (12S and 16SrRNA) genes. Although metazoan mt genomes typically encode 22 transfer RNA genes (tRNAs), the F. cancrivora mtDNA contains 23 tRNAs due to the presence of an extra copy of tRNA(Met). A major noncoding region and a prominent intergenic spacer corresponding to the control region and light-strand replication origin were also found. To confirm the phylogenetic position of F. cancrivora, we compared the gene arrangement with that of other anurans and performed phylogenetic analyses based on mt genomic data. The genome organization of F. cancrivora mtDNA differs from that of typical vertebrates and neobatrachian frogs but is identical with that of F. limnocharis, suggesting that the unique gene arrangement occurred in the common ancestor of the genus. Phylogenetic analyses supported the monophyly of the Fejervarya species used here as well as the dicroglossini clade. Although the family Ranidae as previously recognized (=Ranidae, Discoglossidae, and some other natatanuran families; sensu Frost et al., 2006) is shown as a clade in the maximum parsimony analysis, the maximum likelihood and the Bayesian analyses suggest the paraphyly of the Ranidae with respect to the families, Mantellidae and Rhacophoridae. Three-tandem duplications of gene regions followed by subsequent deletions of supernumerary genes were proposed to explain the evolution of the extra tRNA(Met) and translocation of ND5 from the original neobatrachian gene order.

• Phylogeny and biogeographic diversification of Maianthemum (Ruscaceae: Polygonatae).

  Authors: Ying Meng, Jun Wen, Ze-Long Nie, Hang Sun, Yong-Ping Yang

  Molecular phylogenetics and evolution. 09/2008;

  Maianthemum (Ruscaceae) comprises 28-38 species and includes the two traditionally recognized genera: Maianthemum sensu stricto and Smilacina. Thirty-seven samples representing 22 species ofMaianthemum (Ruscaceae) comprises 28-38 species and includes the two traditionally recognized genera: Maianthemum sensu stricto and Smilacina. Thirty-seven samples representing 22 species of Maianthemum and six closely related outgroup taxa were sequenced for eight chloroplast and nuclear markers (trnL-F, rps16, rpl16, psbA-trnH, rbcL, ndhF, trnK, and ITS) with a total length of nearly 10,000 base pairs. Phylogenetic analyses supported the monophyly of Maianthemum with Maianthemum sensu stricto nested within Smilacina. Almost all species from the eastern Himalayan region in SW China except for Maianthemum tatsienense and M. stenolobum form a well supported clade. This clade is characterized morphologically by short filaments and large anthers, relatively large flowers, and pubescent stems and leaves. Maianthemum tatsienense and M. stenolobum from SW to central China form another clade. The other species from eastern Asia (central to NE China and Japan) and the New World fall into several clades. The intercontinental disjunction between eastern Asia and North America in Maianthemum sensu stricto is estimated to be at 1.68 million years ago (mya) with the Bayesian relaxed clock relaying on uncorrelated rates. A recent radiation at about 2.04mya is suggested in the high mountains of SW China, corresponding to the geographical heterogeneity in that region after the uplift of the Himalayas. Long distance dispersal by birds may have facilitated the evolution of their intercontinental disjunction and their biogeographic diversifications in SW China.

• Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron.

  Authors: Tieyao Tu, Michael O Dillon, Hang Sun, Jun Wen

  Molecular phylogenetics and evolution. 09/2008;

  The phylogeny of Nolana (Solanaceae), a genus primarily distributed in the coastal Atacama and Peruvian deserts with a few species in the Andes and one species endemic to the Galápagos Islands, wasThe phylogeny of Nolana (Solanaceae), a genus primarily distributed in the coastal Atacama and Peruvian deserts with a few species in the Andes and one species endemic to the Galápagos Islands, was reconstructed using sequences of four plastid regions (ndhF, psbA-trnH, rps16-trnK and trnC-psbM) and the nuclear LEAFY second intron. The monophyly of Nolana was strongly supported by all molecular data. The LEAFY data suggested that the Chilean species, including Nolana sessiliflora, the N. acuminata group and at least some members of the Alona group, are basally diverged, supporting the Chilean origin of the genus. Three well-supported clades in the LEAFY tree were corroborated by the SINE (short interspersed elements) or SINE-like insertions. Taxa from Peru are grouped roughly into two clades. Nolana galapagensis from the Galápagos Island is most likely to have derived from a Peruvian ancestor. The monophyly of the morphologically well-diagnosed Nolana acuminata group (N. acuminata, N. baccata, N. paradoxa, N. parviflora, N. pterocarpa, N. rupicola and N. elegans) was supported by both plastid and LEAFY data. Incongruence between the plastid and the LEAFY data was detected concerning primarily the positions of N. sessiliflora, N. galapagensis, taxa of the Alona group and the two Peruvian clades. Such incongruence may be due to reticulate evolution or in some cases lineage sorting of plastid DNA. Incongruence between our previous GBSSI trees and the plastid-LEAFY trees was also detected concerning two well-supported major clades in the GBSSI tree. Duplication of the GBSSI gene may have contributed to this incongruence.

• A preliminary study on population genetic structure and phylogeography of the wild and cultivated Zizania latifolia (Poaceae) based on Adh1a sequences.

  Authors: Xin-Wei Xu, Wei-Dong Ke, Xiao-Ping Yu, Jun Wen, Song Ge

  TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 05/2008; 116(6):835-43.

  Recent decades have witnessed growing interests in exploring the population genetics and phylogeography of crop plants and their wild relatives because of their important value as genetic resources.Recent decades have witnessed growing interests in exploring the population genetics and phylogeography of crop plants and their wild relatives because of their important value as genetic resources. In this study, sequence variation of the nuclear Adh1a gene was used to investigate the genetic diversity and phylogeographic pattern of the wild and cultivated Zizania latifolia Turcz. Sequence data were obtained from 126 individuals representing 21 wild populations in China and 65 varieties of the cultivated Zizania latifolia. Low to medium level nucleotide diversity was found in the wild populations, with northeastern populations being the most variable. We detected significant population subdivision (F (ST) = 0.481) but no significant phylogeogaphical structure, suggesting limited gene flow and dispersal among populations. The current pattern of genetic variation in the wild populations might be explained by a fragmentation of ancient populations due to habitat destruction and degradation during recent decades. The heterogeneous levels and spatial apportionment of genetic diversity among wild populations also suggested a history of gradual colonization of Zizania latifolia populations from the northeast to the south of China. Interestingly, all 65 varieties of the cultivated Zizania latifolia possessed a single identical genotype, implying a single domestication associated with very few initial individuals.

• Phylogenetics and reticulate evolution in Pistacia (Anacardiaceae).

  Authors: Tingshuang Yi, Jun Wen, Avi Golan-Goldhirsh, Dan E Parfitt

  American journal of botany. 02/2008; 95(2):241-51.

  The systematic position and intrageneric relationships of the economically important Pistacia species (Anacardiaceae) are controversial. The phylogeny of Pistacia was assessed using five data sets:The systematic position and intrageneric relationships of the economically important Pistacia species (Anacardiaceae) are controversial. The phylogeny of Pistacia was assessed using five data sets: sequences of nuclear ribosomal ITS, the third intron of the nuclear nitrate reductase gene (NIA-i3), and the plastid ndhF, trnL-F and trnC-trnD. Significant discordance was detected among ITS, NIA-i3, and the combined plastid DNA data sets. ITS, NIA-i3, and the combined plastid data sets were analyzed separately using Bayesian and parsimony methods. Both the ITS and the NIA-i3 data sets resolved the relationships among Pistacia species well; however, these two data sets had significant discordance. The ITS phylogeny best reflects the evolutionary relationships among Pistacia species. Lineage sorting of the NIA-i3 alleles may explain the conflicts between the NIA-i3 and the ITS data sets. The combined analysis of three plastid DNA data sets resolved Pistacia species into three major clades, within which only a few subclades were supported. Pistacia was shown to be monophyletic in all three analyses. The previous intrageneric classification was largely inconsistent with the molecular data. Some Pistacia species appear not to be genealogical species, and evidence for reticulate evolution is presented. Pistacia saportae was shown to be a hybrid with P. lentiscus (maternal) and P. terebinthus (paternal) as the parental taxa.

• Evolution of biogeographic disjunction between eastern Asia and eastern North America in Phryma (Phrymaceae).

  Authors: Ze-Long Nie, Hang Sun, Paul M Beardsley, Richard G Olmstead, Jun Wen

  American journal of botany. 09/2006; 93(9):1343-56.

  This study examines molecular and morphological differentiation in Phryma L., which has only one species with a well-known classic intercontinental disjunct distribution between eastern Asia (EA) andThis study examines molecular and morphological differentiation in Phryma L., which has only one species with a well-known classic intercontinental disjunct distribution between eastern Asia (EA) and eastern North America (ENA). Phylogenetic analysis of nuclear ribosomal ITS and chloroplast rps16 and trnL-F sequences revealed two highly distinct clades corresponding to EA and ENA. The divergence time between the intercontinental populations was estimated to be 3.68 ± 2.25 to 5.23 ± 1.37 million years ago (mya) based on combined chloroplast data using Bayesian and penalized likelihood methods. Phylogeographic and dispersal-vicariance (DIVA) analysis suggest a North American origin of Phryma and its migration into EA via the Bering land bridge. Multivariate analysis based on 23 quantitative morphological characters detected no geographic groups at the intercontinental level. The intercontinental populations of Phryma thus show distinct molecular divergence with little morphological differentiation. The discordance of the molecular and morphological patterns may be explained by morphological stasis due to ecological similarity in both continents. The divergence of Phryma from its close relatives in the Phrymaceae was estimated to be at least 32.32 ± 4.46 to 49.35 ± 3.18 mya.

• Intercontinental biogeography of subfamily Orontioideae (Symplocarpus, Lysichiton, and Orontium) of Araceae in Eastern Asia and North America.

  Authors: Ze-Long Nie, Hang Sun, Heng Li, Jun Wen

  Molecular phylogenetics and evolution. 08/2006; 40(1):155-65.

  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.)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.

• Molecular phylogeny and intra- and intercontinental biogeography of Calycanthaceae.

  Authors: Shiliang Zhou, Susanne S Renner, Jun Wen

  Molecular phylogenetics and evolution. 05/2006; 39(1):1-15.

  Based on nuclear and chloroplast sequences we resolve species relationships in Calycanthaceae and develop a biogeographic hypothesis that explains their intercontinental disjunctions andBased on nuclear and chloroplast sequences we resolve species relationships in Calycanthaceae and develop a biogeographic hypothesis that explains their intercontinental disjunctions and intra-continental diversification in eastern Asia. Fossil-calibrated penalized likelihood and Bayesian divergence time estimates indicate that the Northern Hemisphere Calycanthus and Chimonanthus diverged from each other in the mid-Miocene, while the Australian Idiospermum had already diverged by the Upper Cretaceous and likely represents a remnant of a former Gondwanan distribution of Calycanthaceae that included South America, as indicated by the occurrence of Cretaceous Calycanthaceae fossils in Brazil. Relationships within Calycanthus were difficult to resolve, but a shared 155-bp deletion in the trnL-F intergenic spacer unites the two North American species, which were also sisters in a cpDNA restriction site study. Their ancestor apparently crossed the Bering land bridge in the Miocene. The six species of Chimonanthus, by contrast, diverged from each other as recently as 1-2my ago, and a DIVA analysis with four areas of endemism recognized within China suggests three vicariance and two dispersal events within Chimonanthus, with initial vicariance having occurred between eastern and southwestern or central China. Further divergence then appears to have involved eastern and south-central China, and southwestern and central China.

• Phylogenetic analysis of the grape family (Vitaceae) based on three chloroplast markers.

  Authors: Akiko Soejima, Jun Wen

  American journal of botany. 02/2006; 93(2):278-87.

  Seventy-nine species representing 12 genera of Vitaceae were sequenced for the trnL-F spacer, 37 of which were subsequently sequenced for the atpB-rbcL spacer and the rps16 intron. PhylogeneticSeventy-nine species representing 12 genera of Vitaceae were sequenced for the trnL-F spacer, 37 of which were subsequently sequenced for the atpB-rbcL spacer and the rps16 intron. Phylogenetic analysis of the combined data provided a fairly robust phylogeny for Vitaceae. Cayratia, Tetrastigma, and Cyphostemma form a clade. Cyphostemma and Tetrastigma are each monophyletic, and Cayratia may be paraphyletic. Ampelopsis is paraphyletic with the African Rhoicissus and the South American Cissus striata nested within it. The pinnately leaved Ampelopsis form a subclade, and the simple and palmately leaved Ameplopsis constitutes another with both subclades containing Asian and American species. Species of Cissus from Asia and Central America are monophyletic, but the South American C. striata does not group with other Cissus species. The Asian endemic Nothocissus and Pterisanthes form a clade with Asian Ampelocissus, and A. javalensis from Central America is sister to this clade. Vitis is monophyletic and forms a larger clade with Ampelocissus, Pterisanthes, and Nothocissus. The eastern Asian and North American disjunct Parthenocissus forms a clade with Yua austro-orientalis, a species of a small newly recognized genus from China to eastern Himalaya. Vitaceae show complex multiple intercontinental relationships within the northern hemisphere and between northern and southern hemispheres.

• Monophyly of Kelloggia Torrey ex Benth. (Rubiaceae) and evolution of its intercontinental disjunction between western North America and eastern Asia.

  Authors: Ze-Long Nie, Jun Wen, Hang Sun, Bruce Bartholomew

  American journal of botany. 04/2005; 92(4):642-52.

  Kelloggia Torrey ex Bentham (Rubiaceae) consists of two species disjunctly distributed in western North America (K. galioides Torrey) and the western part of eastern Asia (K. chinensis Franch.). TheKelloggia Torrey ex Bentham (Rubiaceae) consists of two species disjunctly distributed in western North America (K. galioides Torrey) and the western part of eastern Asia (K. chinensis Franch.). The two species exhibit a high level of morphological divergence. To test its monophyly and to infer its biogeographic history, we estimated the phylogeny of Kelloggia and its relatives from sequences of three chloroplast DNA regions (rbcL gene, atpB-rbcL spacer, and rps16 intron). The monophyly of Kelloggia was strongly supported, and it forms a sister relationship with the tribe Rubieae. The divergence time between the two disjunct species of Kelloggia was estimated to be 5.42 ± 2.32 million years ago (mya) using the penalized likelihood method based on rbcL sequence data with fossil calibration. Our result does not support the Madrean-Tethyan hypothesis, which assumes an earlier divergence time of 20-25 mya. Ancestral area analysis, as well as dispersal-vicariance (DIVA) analysis, suggests the Asian origin of Kelloggia and the importance of Eurasia in the diversification of its close relatives in the Rubieae-Theligoneae-Paederieae group. The intercontinental disjunction in Kelloggia is suggested to have evolved via long-distance dispersal from Asia into western North America.