Jun Wen | Smithsonian Institution (original) (raw)

Papers by Jun Wen

Research paper thumbnail of Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication

Molecular biology and evolution, Feb 17, 2016

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes b... more Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ~3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptome and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ~101.6 Mya for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit...

Research paper thumbnail of Aralia frodiniana (Araliaceae), a New Species from Indonesia

Novon, 2001

A new species of Aralia from Sula¬ wesi, Indonesia, A. frodiniana J. Wen, is described and illust... more A new species of Aralia from Sula¬ wesi, Indonesia, A. frodiniana J. Wen, is described and illustrated. The new species belongs to Aralia sect. Dimorphanthus and is similar to A. montana from Java and Sumatra of Indonesia in its short or subsessile petiolules, and the narrowly triangular, dark brownish and glabrous inflorescence bracts with ciliate margins. Aralia frodiniana is distin¬ guished from A. montana by its densely pubescent inflorescence, more pubescent leaves, and thinner leaflets. It differs from A. ferox from Java and Su¬ matra in its pubescent (vs. glabrescent) leaflets, and densely pubescent (vs. glabrous) inflorescence.

Research paper thumbnail of Aralia hiepiana J. Wen & Lowry, a new species of Araliaceae from Vietnam

Wen, Jun, Lowry Ii, Porter P. (2002): Aralia hiepiana J. Wen & Lowry, a new species of Araliaceae... more Wen, Jun, Lowry Ii, Porter P. (2002): Aralia hiepiana J. Wen & Lowry, a new species of Araliaceae from Vietnam. Adansonia (3) 24 (2): 213-216, DOI: http://doi.org/10.5281/zenodo.5180749

Research paper thumbnail of Nurudea zhengii Ren and Qiao, A New Species of the Rhus Gall Aphids (Aphididae: Eriosomatinae: Fordini) from Eastern China

Pakistan Journal of Zoology, 2018

Authors' Contribution ZR collected the samples, observed the morphological characters and drafted... more Authors' Contribution ZR collected the samples, observed the morphological characters and drafted the manuscript. XS performed the experiments, analyzed and interpreted the data. CDD and JW revised and polished the manuscript.

Research paper thumbnail of Complete mitochondrial genome of the witch-hazel leaf gall aphid Hamamelistes spinosus (Hemiptera: Aphididae: Hormaphidinae)

Mitochondrial DNA Part B, 2020

We sequenced the complete mitochondrial genome of Hamamelistes spinosus using the shotgun genome-... more We sequenced the complete mitochondrial genome of Hamamelistes spinosus using the shotgun genome-skimming method. The mitogenome of H. spinosus is 15,089 bp in length with a much higher A þ T content of 81.8% than that of G þ C (18.2%) and consists of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. All the 13 PCGs initiate with a typical ATN and end with TAA except for two genes COX1 and ND4, which terminate with a single T. All the tRNAs form a classical cloverleaf secondary structure except for tRNA-Ser (AGN), which does not have the dihydrouridine (DHU) arm. In addition, we constructed the phylogenetic tree of Aphididae with two species Adelges laricis and Daktulosphaira vitifoliae as outgroups and the results showed that Hamamelistes spinosus is sister to Hormaphis betulae and they are closely allied with Neothoracaphis yanonis.

Research paper thumbnail of The complete chloroplast genome sequence of Oxytropis bicolour Bunge (Fabaceae)

Mitochondrial DNA Part B, 2019

The first complete chloroplast genome of Oxytropis bicolour Bunge is reported and characterized i... more The first complete chloroplast genome of Oxytropis bicolour Bunge is reported and characterized in this study. The whole chloroplast genome was 122,461 base pairs in length with 110 genes, including 76 protein-coding genes, 30 tRNAs, and 4 rRNAs. In addition, the atpF intron was absent. Maximumlikelihood (ML) phylogenetic analysis indicated that O. bicolour and species of Astragalus were closely related, which is congruent with previous studies.

Research paper thumbnail of Awards of JSE Outstanding Papers (2017)

Journal of Systematics and Evolution, 2019

Research paper thumbnail of Floral organogenesis of Prunus laurocerasus and P. serotina and its significance for the systematics of the genus and androecium diversity in Rosaceae

Botany, 2018

Phylogenetic studies have shown that most clades in Prunus are well-supported by the flower struc... more Phylogenetic studies have shown that most clades in Prunus are well-supported by the flower structure, but most taxa in the racemose group have not yet been re-evaluated and could contribute to the understanding of the systematic relationships of the subgenera. We examined the inflorescence and flower development in Prunus laurocerasus L. (subgenus Laurocerasus) and P. serotina Ehrh. (subgenus Padus I) using scanning electron microscopy. Our results indicate that they share several floral development characters but differ in the following aspects: (i) all of their flowers are fully developed and each flower is enclosed by a bract and two bracteoles, which later stop development (vs. the terminal flower degenerates and only a single bract subtends each flower); (ii) the style protrudes from the floral bud (vs. the style is crooked and below the anthers); (iii) the outer integument initiates close to the inner one (vs. in the middle of the ovule); and (iv) an obturator appears after i...

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

Theoretical and Applied Genetics, 2008

Research paper thumbnail of Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications

Gene, 2009

The complete nucleotide sequence of the mitochondrial (mt) genome of the crab-eating frog, Fejerv... more 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 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.

Research paper thumbnail of Cryptic Dioecy in Nyssa Yunnanensis (Nyssaceae), A Critically Endangered Species from Tropical Eastern Asia1

Annals of the Missouri Botanical Garden, 2009

Research paper thumbnail of First fossil record of Staphylea L. (Staphyleaceae) from North America, and its biogeographic implications

Plant Systematics and Evolution, 2015

Research paper thumbnail of A synopsis of the expanded Rhaphiolepis (Maleae, Rosaceae)

PhytoKeys, 2020

As part of the integrative systematic studies on the tribe Maleae, a synopsis of the expanded Rha... more As part of the integrative systematic studies on the tribe Maleae, a synopsis of the expanded Rhaphiolepis is presented, recognizing 45 species. Three new forms were validated: R. bengalensis f. contracta B.B.Liu & J.Wen, R. bengalensis f. intermedia B.B.Liu & J.Wen, and R. bengalensis f. multinervata B.B.Liu & J.Wen, and four new combinations are made here: R. bengalensis f. angustifolia (Cardot) B.B.Liu & J.Wen, R. bengalensis f. gigantea (J.E.Vidal) B.B.Liu & J.Wen, R. laoshanica (W.B.Liao, Q.Fan & S.F.Chen) B.B.Liu & J.Wen, and R. latifolia (Hook.f.) B.B.Liu & J.Wen. Furthermore, one new name, Rhaphiolepis yui B.B.Liu & J.Wen is proposed here, and three taxa were reduced as new synonyms. We also provide lectotypification for 13 names: Crataegus bibas, Eriobotrya philippinensis, Mespilus spiralis, Opa integerrima, Photinia luzonensis, Rhaphiolepis brevipetiolata, R. ferruginea var. serrata, R. fragrans, R. gracilis, R. hainanensis, R. kerrii, R. indica subsp. umbellata var. liuki...

Research paper thumbnail of Typification of 23 names in Eriobotrya (Maleae, Rosaceae)

PhytoKeys, 2020

As part of a comprehensive systematic study on the genusEriobotryaand its close relatives from th... more As part of a comprehensive systematic study on the genusEriobotryaand its close relatives from the E & SE Asia, new typifications of 23 names are presented here, along with some nomenclatural notes of the names involved. We lectotypified 22 names including accepted names and synonyms. They are:E. acuminatissima, E. bengalensis var. angustifolia; E. bengalensis f. intermedia,E. brackloi, E. brackloi var. atrichophylla, E. elliptica var. petelotii, E. fragrans var. furfuracea,E. glabrescens,E. grandiflora,E. henryi,E. oblongifolia,E. petiolata,E. platyphylla,E. poilanei,E. prinoides, E. prinoides var. laotica,E. salwinensis,E. serrata,E. stipularis,Hiptage cavaleriei,Photinia longifolia,Symplocos seguinii. One neotype ofPhotinia dubiawas also proposed in this study, andE. pseudoraphiolepisandMespilus cuilawere identified as superfluous names. In addition, we also summarized the typification of 18 names for taxonomic reference:E. angustissima,E. balgooyi,E. condaoensis,E. × daduheensis...

Research paper thumbnail of Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram

Annals of botany, 2011

Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morpho... more Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa. Two low-copy nuclear (LCN) markers, Pepc4 and EF-1α, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) using the Bayesian dating method. The monophyly of Eleusine is strongly supported by sequence data from two LCN markers. In the cpDNA phylogeny, three tetraploid species (E. africana, E. coracana and E. kigeziensis) share a common ancestor with the E. indica-E. tristachya clade, which is consid...

Research paper thumbnail of A taxonomic synopsis of Altingiaceae with nine new combinations

Research paper thumbnail of Phylogeny of Nolana (Nolaneae, Solanoideae, Solanaceae) as inferred from granule-bound starch synthase I (GBSSI) sequences

Research paper thumbnail of Molecular phylogenetic analysis of Leibnitzia Cass. (Asteraceae: Mutisieae: Gerbera-complex), an Asian-North American disjunct genus

Journal of Systematics and Evolution, 2010

Leibnitzia comprises six species of perennial herbs that are adapted to high elevation conditions... more Leibnitzia comprises six species of perennial herbs that are adapted to high elevation conditions and is one of only two Asteraceae genera known to have an exclusively disjunct distribution spanning central to eastern Asia and North America. Molecular phylogenetic analysis of Leibnitzia and other Gerbera-complex members indicates that Leibnitzia is monophyletic, which is in contrast with our expectation that the American Leibnitzia species L. lyrata and L. occimadrensis would be more closely related to another American member of the Gerbera-covaplex, namely Chaptalia. Ancestral area reconstructions show that the historical biogeography of the Gerbera-covaplex mirrors that of the entire Asteraceae, with early diverging lineages located in South America that were followed by transfers to Africa and Eurasia and most recently, to North America. Intercontinental transfer of Leibnitzia appears to have been directed from Asia to North America. Independent calibrations of nuclear (ribosomal DNA internal transcribed spacer region) and chloroplast (trnL-rpl32 intron) DNA sequence data using relaxed clock methods and either mean rate or fossil-based priors unanimously support Miocene and younger divergence times for Gerbera-covaplex taxa. The ages are not consistent with most Gondwanan vicariance episodes and thus, the global distribution of Gerbera-covaplex members must be explained in large part by long-distance dispersal. American species of Leibnitzia are estimated to have diverged from their Asian ancestor during the Quaternary (ca. 2 mya) and either migrated overland to North America via Beringia and retreated southwards along high elevation corridors to their present location in southwestern North America or were dispersed long distance.

Research paper thumbnail of Systematics and biogeography of the non-viny grape relative Leea (Vitaceae)

Botanical Journal of the Linnean Society, 2012

Leea, sometimes treated as the monogeneric family Leeaceae, is sister to the rest of the grape fa... more Leea, sometimes treated as the monogeneric family Leeaceae, is sister to the rest of the grape family, Vitaceae, but its systematics is poorly known. Phylogenetic relationships in Leea were reconstructed with parsimony and Bayesian methods using nuclear ribosomal sequences to assess species circumscriptions, morphological evolution and biogeography. The internal transcribed spacer secondary structure model for Leea facilitated homology assessments during sequence alignment. Nine morphological characters were mapped onto the phylogenetic tree. Four major clades in Leea were supported, with L. asiatica s.l. (=clade I) as the earliest diverging clade and having plesiomorphic free stamens. Clade II, which includes the prickle-bearing species, is sister to clade III, which includes species with comparatively large flowers. Clade IV, sister to clade II + III, was resolved into four subclades. Each subclade included accessions of L. indica and L. guineensis intermixed with six other morphologically distinct species, showing the polyphyly of these two species as currently circumscribed. Flower colour, previously used to characterize species, was shown to be unreliable for species identification. Dating analyses estimated that Leea originated in Indochina in the Late Cretaceous (65-86.19 Mya, 95% highest posterior density). The members of the major clades later spread to India, Africa, Madagascar, SouthEast (SE) Asia and tropical Australasia. Major species diversification occurred in the Neogene, when dynamic environmental and geological changes in SE Asia presented new ecological niches.

Research paper thumbnail of Systematic placement and biogeographical relationships of the monotypic generaGypothamniumandOxyphyllum(Asteraceae: Mutisioideae) from the Atacama Desert

Botanical Journal of the Linnean Society, 2009

Gypothamnium and Oxyphyllum (Asteraceae) are two monotypic genera endemic to the Atacama Desert o... more Gypothamnium and Oxyphyllum (Asteraceae) are two monotypic genera endemic to the Atacama Desert of northern Chile. We performed a phylogenetic analysis using published sequences of the plastid rbcL and ndhF genes, the trnL-trnF region and the nuclear ribosomal internal transcribed spacer (ITS) to assess the systematic placement of the two genera within Mutisioideae. On the basis of the phylogenetic results, we constructed area cladograms to explore the biogeographical relationships and origin of the genera. The phylogenetic analysis showed that Gypothamnium is closely related to Aphylloclados, Plazia, Urmenetia, Lycoseris and Onoseris, whereas Oxyphyllum is closely related to Leucheria, Moscharia, Polyachyrus and, with low support, Jungia. These results do not differ substantially from those proposed in previous treatments based on morphological characters. The biogeographical analysis suggests that Gypothamnium in the coastal Atacama Desert is related to taxa that are currently distributed in eastern subtropical South America and in the Puna. Oxyphyllum may have originated from central Chile and other areas in southern South America, but its sister group (Leucheria + Polyachyrus) also reaches the Puna and the coastal Atacama Desert. Both groups show ancestral affinities with elements currently distributed in northwestern South America and Mesoamerica.

Research paper thumbnail of Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication

Molecular biology and evolution, Feb 17, 2016

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes b... more Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ~3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptome and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ~101.6 Mya for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit...

Research paper thumbnail of Aralia frodiniana (Araliaceae), a New Species from Indonesia

Novon, 2001

A new species of Aralia from Sula¬ wesi, Indonesia, A. frodiniana J. Wen, is described and illust... more A new species of Aralia from Sula¬ wesi, Indonesia, A. frodiniana J. Wen, is described and illustrated. The new species belongs to Aralia sect. Dimorphanthus and is similar to A. montana from Java and Sumatra of Indonesia in its short or subsessile petiolules, and the narrowly triangular, dark brownish and glabrous inflorescence bracts with ciliate margins. Aralia frodiniana is distin¬ guished from A. montana by its densely pubescent inflorescence, more pubescent leaves, and thinner leaflets. It differs from A. ferox from Java and Su¬ matra in its pubescent (vs. glabrescent) leaflets, and densely pubescent (vs. glabrous) inflorescence.

Research paper thumbnail of Aralia hiepiana J. Wen & Lowry, a new species of Araliaceae from Vietnam

Wen, Jun, Lowry Ii, Porter P. (2002): Aralia hiepiana J. Wen & Lowry, a new species of Araliaceae... more Wen, Jun, Lowry Ii, Porter P. (2002): Aralia hiepiana J. Wen & Lowry, a new species of Araliaceae from Vietnam. Adansonia (3) 24 (2): 213-216, DOI: http://doi.org/10.5281/zenodo.5180749

Research paper thumbnail of Nurudea zhengii Ren and Qiao, A New Species of the Rhus Gall Aphids (Aphididae: Eriosomatinae: Fordini) from Eastern China

Pakistan Journal of Zoology, 2018

Authors' Contribution ZR collected the samples, observed the morphological characters and drafted... more Authors' Contribution ZR collected the samples, observed the morphological characters and drafted the manuscript. XS performed the experiments, analyzed and interpreted the data. CDD and JW revised and polished the manuscript.

Research paper thumbnail of Complete mitochondrial genome of the witch-hazel leaf gall aphid Hamamelistes spinosus (Hemiptera: Aphididae: Hormaphidinae)

Mitochondrial DNA Part B, 2020

We sequenced the complete mitochondrial genome of Hamamelistes spinosus using the shotgun genome-... more We sequenced the complete mitochondrial genome of Hamamelistes spinosus using the shotgun genome-skimming method. The mitogenome of H. spinosus is 15,089 bp in length with a much higher A þ T content of 81.8% than that of G þ C (18.2%) and consists of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. All the 13 PCGs initiate with a typical ATN and end with TAA except for two genes COX1 and ND4, which terminate with a single T. All the tRNAs form a classical cloverleaf secondary structure except for tRNA-Ser (AGN), which does not have the dihydrouridine (DHU) arm. In addition, we constructed the phylogenetic tree of Aphididae with two species Adelges laricis and Daktulosphaira vitifoliae as outgroups and the results showed that Hamamelistes spinosus is sister to Hormaphis betulae and they are closely allied with Neothoracaphis yanonis.

Research paper thumbnail of The complete chloroplast genome sequence of Oxytropis bicolour Bunge (Fabaceae)

Mitochondrial DNA Part B, 2019

The first complete chloroplast genome of Oxytropis bicolour Bunge is reported and characterized i... more The first complete chloroplast genome of Oxytropis bicolour Bunge is reported and characterized in this study. The whole chloroplast genome was 122,461 base pairs in length with 110 genes, including 76 protein-coding genes, 30 tRNAs, and 4 rRNAs. In addition, the atpF intron was absent. Maximumlikelihood (ML) phylogenetic analysis indicated that O. bicolour and species of Astragalus were closely related, which is congruent with previous studies.

Research paper thumbnail of Awards of JSE Outstanding Papers (2017)

Journal of Systematics and Evolution, 2019

Research paper thumbnail of Floral organogenesis of Prunus laurocerasus and P. serotina and its significance for the systematics of the genus and androecium diversity in Rosaceae

Botany, 2018

Phylogenetic studies have shown that most clades in Prunus are well-supported by the flower struc... more Phylogenetic studies have shown that most clades in Prunus are well-supported by the flower structure, but most taxa in the racemose group have not yet been re-evaluated and could contribute to the understanding of the systematic relationships of the subgenera. We examined the inflorescence and flower development in Prunus laurocerasus L. (subgenus Laurocerasus) and P. serotina Ehrh. (subgenus Padus I) using scanning electron microscopy. Our results indicate that they share several floral development characters but differ in the following aspects: (i) all of their flowers are fully developed and each flower is enclosed by a bract and two bracteoles, which later stop development (vs. the terminal flower degenerates and only a single bract subtends each flower); (ii) the style protrudes from the floral bud (vs. the style is crooked and below the anthers); (iii) the outer integument initiates close to the inner one (vs. in the middle of the ovule); and (iv) an obturator appears after i...

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

Theoretical and Applied Genetics, 2008

Research paper thumbnail of Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications

Gene, 2009

The complete nucleotide sequence of the mitochondrial (mt) genome of the crab-eating frog, Fejerv... more 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 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.

Research paper thumbnail of Cryptic Dioecy in Nyssa Yunnanensis (Nyssaceae), A Critically Endangered Species from Tropical Eastern Asia1

Annals of the Missouri Botanical Garden, 2009

Research paper thumbnail of First fossil record of Staphylea L. (Staphyleaceae) from North America, and its biogeographic implications

Plant Systematics and Evolution, 2015

Research paper thumbnail of A synopsis of the expanded Rhaphiolepis (Maleae, Rosaceae)

PhytoKeys, 2020

As part of the integrative systematic studies on the tribe Maleae, a synopsis of the expanded Rha... more As part of the integrative systematic studies on the tribe Maleae, a synopsis of the expanded Rhaphiolepis is presented, recognizing 45 species. Three new forms were validated: R. bengalensis f. contracta B.B.Liu & J.Wen, R. bengalensis f. intermedia B.B.Liu & J.Wen, and R. bengalensis f. multinervata B.B.Liu & J.Wen, and four new combinations are made here: R. bengalensis f. angustifolia (Cardot) B.B.Liu & J.Wen, R. bengalensis f. gigantea (J.E.Vidal) B.B.Liu & J.Wen, R. laoshanica (W.B.Liao, Q.Fan & S.F.Chen) B.B.Liu & J.Wen, and R. latifolia (Hook.f.) B.B.Liu & J.Wen. Furthermore, one new name, Rhaphiolepis yui B.B.Liu & J.Wen is proposed here, and three taxa were reduced as new synonyms. We also provide lectotypification for 13 names: Crataegus bibas, Eriobotrya philippinensis, Mespilus spiralis, Opa integerrima, Photinia luzonensis, Rhaphiolepis brevipetiolata, R. ferruginea var. serrata, R. fragrans, R. gracilis, R. hainanensis, R. kerrii, R. indica subsp. umbellata var. liuki...

Research paper thumbnail of Typification of 23 names in Eriobotrya (Maleae, Rosaceae)

PhytoKeys, 2020

As part of a comprehensive systematic study on the genusEriobotryaand its close relatives from th... more As part of a comprehensive systematic study on the genusEriobotryaand its close relatives from the E & SE Asia, new typifications of 23 names are presented here, along with some nomenclatural notes of the names involved. We lectotypified 22 names including accepted names and synonyms. They are:E. acuminatissima, E. bengalensis var. angustifolia; E. bengalensis f. intermedia,E. brackloi, E. brackloi var. atrichophylla, E. elliptica var. petelotii, E. fragrans var. furfuracea,E. glabrescens,E. grandiflora,E. henryi,E. oblongifolia,E. petiolata,E. platyphylla,E. poilanei,E. prinoides, E. prinoides var. laotica,E. salwinensis,E. serrata,E. stipularis,Hiptage cavaleriei,Photinia longifolia,Symplocos seguinii. One neotype ofPhotinia dubiawas also proposed in this study, andE. pseudoraphiolepisandMespilus cuilawere identified as superfluous names. In addition, we also summarized the typification of 18 names for taxonomic reference:E. angustissima,E. balgooyi,E. condaoensis,E. × daduheensis...

Research paper thumbnail of Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram

Annals of botany, 2011

Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morpho... more Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa. Two low-copy nuclear (LCN) markers, Pepc4 and EF-1α, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) using the Bayesian dating method. The monophyly of Eleusine is strongly supported by sequence data from two LCN markers. In the cpDNA phylogeny, three tetraploid species (E. africana, E. coracana and E. kigeziensis) share a common ancestor with the E. indica-E. tristachya clade, which is consid...

Research paper thumbnail of A taxonomic synopsis of Altingiaceae with nine new combinations

Research paper thumbnail of Phylogeny of Nolana (Nolaneae, Solanoideae, Solanaceae) as inferred from granule-bound starch synthase I (GBSSI) sequences

Research paper thumbnail of Molecular phylogenetic analysis of Leibnitzia Cass. (Asteraceae: Mutisieae: Gerbera-complex), an Asian-North American disjunct genus

Journal of Systematics and Evolution, 2010

Leibnitzia comprises six species of perennial herbs that are adapted to high elevation conditions... more Leibnitzia comprises six species of perennial herbs that are adapted to high elevation conditions and is one of only two Asteraceae genera known to have an exclusively disjunct distribution spanning central to eastern Asia and North America. Molecular phylogenetic analysis of Leibnitzia and other Gerbera-complex members indicates that Leibnitzia is monophyletic, which is in contrast with our expectation that the American Leibnitzia species L. lyrata and L. occimadrensis would be more closely related to another American member of the Gerbera-covaplex, namely Chaptalia. Ancestral area reconstructions show that the historical biogeography of the Gerbera-covaplex mirrors that of the entire Asteraceae, with early diverging lineages located in South America that were followed by transfers to Africa and Eurasia and most recently, to North America. Intercontinental transfer of Leibnitzia appears to have been directed from Asia to North America. Independent calibrations of nuclear (ribosomal DNA internal transcribed spacer region) and chloroplast (trnL-rpl32 intron) DNA sequence data using relaxed clock methods and either mean rate or fossil-based priors unanimously support Miocene and younger divergence times for Gerbera-covaplex taxa. The ages are not consistent with most Gondwanan vicariance episodes and thus, the global distribution of Gerbera-covaplex members must be explained in large part by long-distance dispersal. American species of Leibnitzia are estimated to have diverged from their Asian ancestor during the Quaternary (ca. 2 mya) and either migrated overland to North America via Beringia and retreated southwards along high elevation corridors to their present location in southwestern North America or were dispersed long distance.

Research paper thumbnail of Systematics and biogeography of the non-viny grape relative Leea (Vitaceae)

Botanical Journal of the Linnean Society, 2012

Leea, sometimes treated as the monogeneric family Leeaceae, is sister to the rest of the grape fa... more Leea, sometimes treated as the monogeneric family Leeaceae, is sister to the rest of the grape family, Vitaceae, but its systematics is poorly known. Phylogenetic relationships in Leea were reconstructed with parsimony and Bayesian methods using nuclear ribosomal sequences to assess species circumscriptions, morphological evolution and biogeography. The internal transcribed spacer secondary structure model for Leea facilitated homology assessments during sequence alignment. Nine morphological characters were mapped onto the phylogenetic tree. Four major clades in Leea were supported, with L. asiatica s.l. (=clade I) as the earliest diverging clade and having plesiomorphic free stamens. Clade II, which includes the prickle-bearing species, is sister to clade III, which includes species with comparatively large flowers. Clade IV, sister to clade II + III, was resolved into four subclades. Each subclade included accessions of L. indica and L. guineensis intermixed with six other morphologically distinct species, showing the polyphyly of these two species as currently circumscribed. Flower colour, previously used to characterize species, was shown to be unreliable for species identification. Dating analyses estimated that Leea originated in Indochina in the Late Cretaceous (65-86.19 Mya, 95% highest posterior density). The members of the major clades later spread to India, Africa, Madagascar, SouthEast (SE) Asia and tropical Australasia. Major species diversification occurred in the Neogene, when dynamic environmental and geological changes in SE Asia presented new ecological niches.

Research paper thumbnail of Systematic placement and biogeographical relationships of the monotypic generaGypothamniumandOxyphyllum(Asteraceae: Mutisioideae) from the Atacama Desert

Botanical Journal of the Linnean Society, 2009

Gypothamnium and Oxyphyllum (Asteraceae) are two monotypic genera endemic to the Atacama Desert o... more Gypothamnium and Oxyphyllum (Asteraceae) are two monotypic genera endemic to the Atacama Desert of northern Chile. We performed a phylogenetic analysis using published sequences of the plastid rbcL and ndhF genes, the trnL-trnF region and the nuclear ribosomal internal transcribed spacer (ITS) to assess the systematic placement of the two genera within Mutisioideae. On the basis of the phylogenetic results, we constructed area cladograms to explore the biogeographical relationships and origin of the genera. The phylogenetic analysis showed that Gypothamnium is closely related to Aphylloclados, Plazia, Urmenetia, Lycoseris and Onoseris, whereas Oxyphyllum is closely related to Leucheria, Moscharia, Polyachyrus and, with low support, Jungia. These results do not differ substantially from those proposed in previous treatments based on morphological characters. The biogeographical analysis suggests that Gypothamnium in the coastal Atacama Desert is related to taxa that are currently distributed in eastern subtropical South America and in the Puna. Oxyphyllum may have originated from central Chile and other areas in southern South America, but its sister group (Leucheria + Polyachyrus) also reaches the Puna and the coastal Atacama Desert. Both groups show ancestral affinities with elements currently distributed in northwestern South America and Mesoamerica.