Publications by authors named "Ze-Long Nie"

35 Publications

Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae.

Mol Phylogenet Evol 2021 Oct 17;163:107235. Epub 2021 Jun 17.

Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China. Electronic address:

The inverted repeat-lacking clade (IRLC) is one of the most derived clades within the subfamily Papilionoideae of the legume family, and includes various economically important plants, e.g., chickpeas, peas, liquorice, and the largest genus of angiosperms, Astragalus. Tribe Wisterieae is one of the earliest diverged groups of the IRLC, and its generic delimitation and spatiotemporal diversification needs further clarifications. Based on genome skimming data, we herein reconstruct the phylogenomic framework of the IRLC, and infer the inter-generic relationships and historical biogeography of Wisterieae. We redefine tribe Caraganeae to contain Caragana only, and tribe Astragaleae is reduced to the Erophaca-Astragalean clade. The chloroplast capture scenario was hypothesized as the most plausible explanation of the topological incongruences between the chloroplast CDSs and nuclear ribosomal DNA trees in both the Glycyrrhizinae-Adinobotrys-Wisterieae clade and the Chesneyeae-Caraganeae-Hedysareae clade. A new name, Caragana lidou L. Duan & Z.Y. Chang, is proposed within Caraganeae. Thirteen genera are herein supported within Wisterieae, including a new genus, Villosocallerya L. Duan, J. Compton & Schrire, segregated from Callerya. Our biogeographic analyses suggest that Wisterieae originated in the late Eocene and its most recent common ancestor (MRCA) was distributed in continental southeastern Asia. Lineages of Wisterieae remained in the ancestral area from the early Oligocene to the early Miocene. By the middle Miocene, Whitfordiodendron and the MRCA of Callerya-Kanburia-Villosocallerya Clade became disjunct between the Sunda area and continental southeastern Asia, respectively; the MRCA of Wisteria migrated to North America via the Bering land bridge. The ancestor of Austrocallerya and Padbruggea migrated to the Wallacea-Oceania area, which split in the early Pliocene. In the Pleistocene, Wisteria brachybotrys, W. floribunda and Wisteriopsis japonica reached Japan, and Callerya cinerea dispersed to South Asia. This study provides a solid phylogenomic for further evolutionary/biogeographic/systematic investigations on the ecologically diverse and economically important IRLC legumes.
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http://dx.doi.org/10.1016/j.ympev.2021.107235DOI Listing
October 2021

Phylogeny and biogeography of (Asparagaceae: Nolinoideae) revisited with emphasis on its divergence pattern in SW China.

Plant Divers 2021 Apr 10;43(2):93-101. Epub 2021 Feb 10.

Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China.

is a genus with more than 35 species from the tribe Polygonateae (Asparagaceae), widely distributed between North to Central Americas and eastern Asia with high diversity in the eastern Himalayas to the Hengduan Mountains of SW China. Although most species from SW China form a well-supported clade, phylogenetic relationships within this clade remain unclear. With a broad level of taxon sampling and an extensive character sampling from eight DNA regions, this study intends to revisit the phylogeny and biogeography of the genus to better understand the divergence patterns of species from SW China. Phylogenetic results suggested the monophyly of with recognition of nine strongly supported clades, but backbone relationships among these clades remained largely uncertain. For the SW China clade, individuals from the same species are grouped into different lineages. Our results revealed that the fast radiation of the SW China clade was occurred in the eastern Himalayas, followed by subsequent radiation in the Hengduan Mountains in the Pliocene. Intercontinental disjunctions of in the Northern Hemisphere appear to have occurred multiple times during the late Miocene to the Pliocene, likely resulted by a combination of both vicariance and long-distance dispersal events.
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http://dx.doi.org/10.1016/j.pld.2021.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8103418PMC
April 2021

Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae.

Mol Phylogenet Evol 2021 09 14;162:107202. Epub 2021 May 14.

Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA. Electronic address:

The tribe Senecioneae is one of the largest tribes in Asteraceae, with a nearly cosmopolitan distribution. Despite great efforts devoted to elucidate the evolution of Senecioneae, many questions still remain concerning the systematics of this group, from the tribal circumscription and position to species relationships in many genera. The hybridization-based target enrichment method of next-generation sequencing has been accepted as a promising approach to resolve phylogenetic problems. We herein develop a set of single-/low-copy genes for Senecioneae, and test their phylogenetic utilities. Our results demonstrate that these genes work highly efficiently for Senecioneae, with a high average gene recovery of 98.8% across the tribe and recovering robust phylogenetic hypotheses at different levels. In particular, the delimitation of the Senecioneae has been confirmed to include Abrotanella and exclude Doronicum, with the former sister to core Senecioneae and the latter shown to be more closely related to Calenduleae. Moreover, Doronicum and Calenduleae are inferred to be the closest relatives of Senecioneae, which is a new hypothesis well supported by statistical topology tests, morphological evidence, and the profile of pyrrolizidine alkaloids, a special kind of chemical characters generally used to define Senecioneae. Furthermore, this study suggests a complex reticulation history in the diversification of Senecioneae, accounting for the prevalence of polyploid groups in the tribe. With subtribe Tussilagininae s.str. as a case study showing a more evident pattern of gene duplication, we further explored reconstructing the phylogeny in the groups with high ploidy levels. Our results also demonstrate that tree topologies based on sorted paralogous copies are stable across different methods of phylogenetic inference, and more congruent with the morphological evidence and the results of previous phylogenetic studies.
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http://dx.doi.org/10.1016/j.ympev.2021.107202DOI Listing
September 2021

The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data.

Front Plant Sci 2020 14;11:584981. Epub 2021 Jan 14.

Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, China.

The subfamily Nolinoideae of Asparagaceae is an extremely morphologically heterogeneous group, which is comprised of seven lineages, formerly known as Eriospermaceae, Polygonateae, Ophiopogoneae, Convallarieae, Ruscaceae s.s., Dracaenaceae, and Nolinaceae from different families or even orders. Their drastically divergent morphologies and low level of molecular resolution have hindered our understanding on their evolutionary history. To resolve reliable and clear phylogenetic relationships of the Nolinoideae, a phylogenetic study was conducted based on transcriptomic sequencing of 15 species representing all the seven lineages. A dataset containing up to 2,850,331 sites across 2,126 genes was analyzed using both concatenated and coalescent methods. Except for as outgroup, the transcriptomic data strongly resolved the remaining six lineages into two groups, one is a paraphyletic grade including the woody lineages of dracaenoids, ruscoids, and nolinoids and a monophyletic herbaceous clade. Within the herbaceous group, the Ophiopogoneae + is sister to a clade that is composed of Convallarieae and the monophyletic Polygonateae. Our work provides a first robust deep relationship of the highly heterogeneous Nolinoideae and paves the way for further investigations of its complex evolution.
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http://dx.doi.org/10.3389/fpls.2020.584981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7840527PMC
January 2021

Phylogenomic relationships and character evolution of the grape family (Vitaceae).

Mol Phylogenet Evol 2021 01 29;154:106948. Epub 2020 Aug 29.

Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C. 20013-7012, USA. Electronic address:

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.
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http://dx.doi.org/10.1016/j.ympev.2020.106948DOI Listing
January 2021

Data of assembly and annotation of transcriptome from (Asparagaceae: Nolinoideae).

Data Brief 2020 Aug 21;31:105738. Epub 2020 May 21.

Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, 416000, China.

is a large genus of herbaceous plants with more than 130 species growing in tropical forests of SE Asia and specially diversified in southern China and northern Vietnam. The genus is characterized by its evergreen understorey habitats with flowers set at ground level and more or less hidden in litter material. is a species currently only known from central China. In recent years, number of species in this genus has been greatly increased. However, the high throughput sequencing data have never been reported in this genus. Here, we sequenced the transcriptome of obtained from young leaves using the Illumina HiSeq2000 with 9.15Gb of clean data. Because of the absence of a reference-grade genome in the genus, a assembly of the transcriptome data with full annotation have been carried out. This data is accessible via NCBI BioProject (PRJNA608213).
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http://dx.doi.org/10.1016/j.dib.2020.105738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7276517PMC
August 2020

The importance of the North Atlantic land bridges and eastern Asia in the post-Boreotropical biogeography of the Northern Hemisphere as revealed from the poison ivy genus (Toxicodendron, Anacardiaceae).

Mol Phylogenet Evol 2019 10 13;139:106561. Epub 2019 Jul 13.

Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China. Electronic address:

The Northern Hemisphere was widely covered by a tropical flora (i.e., the Boretropical flora) in the Eocene and the evaluation of plant diversifications in the post-Boreotropical era has become an important challenge to understanding the modern biogeographic complexity in this vast region. Toxicodendron or the poison ivy genus of the sumac family has a temperate to tropical distribution in Asia and North America and can serve as an excellent model for investigating the evolution of the post-Boreotropical biogeographic complexity. Molecular age estimates were calculated using a Bayesian approach with sampling covering the taxonomic diversity and biogeographic distributions within the genus, and sequence data from three nuclear DNA (ITS, ETS, NIA-i3) and two chloroplast (ndhF, trnL-F) regions, combined with calibrations from three fossil records. Ancestral areas were reconstructed using RASP and BioGeoBears. Toxicodendron is estimated to have a Boreotropical origin in the New World in the late Eocene at 37.68 Ma. It then diversified into a subtropical-temperate and a tropical lineage, followed by migrating into eastern Asia via the North Atlantic land bridges in the Oligocene to early Miocene. Two tropical migration events during the Miocene are identified between continental Asia and SE Asia or New Guinea around 20.91 Ma and 14.33 Ma, respectively. Results from this study highlight the importance of the North Atlantic land bridges and eastern Asia in the post-Boreotopical plant divergences in the Northern Hemisphere, especially when biogeographic exchanges between North and South America were limited.
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http://dx.doi.org/10.1016/j.ympev.2019.106561DOI Listing
October 2019

Phylogenomics, biogeography, and adaptive radiation of grapes.

Mol Phylogenet Evol 2018 12 6;129:258-267. Epub 2018 Sep 6.

Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China. Electronic address:

The application of whole-genome resequencing based on next-generation sequencing technologies provides an unprecedented opportunity for researchers to resolve long-standing evolutionary problems. Taxa belonging to the grape genus (Vitis L.) represent important genetic resources for the improvement of cultivated grapes. However, it has been challenging to resolve the deep phylogenetic relationships within Vitis, limiting the current understanding of the evolutionary history of Vitis and preventing the use of valuable wild grape resources. In this study, we obtained whole-genome sequence data from 41 accessions representing most taxa within subgenus Vitis and aligned these sequences to the Vitis vinifera L. reference genome. We reconstructed deep phylogenetic relationships within subgenus Vitis based on 2068 single-copy orthologous genes, which led to a robust topology with bootstrap support values of 100% for almost all branches. Three main clades are recovered within subgenus Vitis reflecting their continental distribution through North America, Europe, and East Asia, respectively. Our results suggest that the most possible migration route of the East Asian Vitis is from northeastern Asia southward to South Asia and Southeast Asia. The East Asian Vitis seems to have experienced adaptive radiation during the Miocene. This study provides novel insights into the diversification history of the grape genus Vitis.
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http://dx.doi.org/10.1016/j.ympev.2018.08.021DOI Listing
December 2018

Molecular phylogeny of Galium L. of the tribe Rubieae (Rubiaceae) - Emphasis on Chinese species and recognition of a new genus Pseudogalium.

Mol Phylogenet Evol 2018 09 5;126:221-232. Epub 2018 Apr 5.

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. Electronic address:

Galium L. is the largest genus in the tribe Rubieae, with about 667 species distributed worldwide. Previous researches mainly focused on species from the Americas and Europe. In the present paper, we greatly increased the number of samples examined from eastern Asia (especially China), representing the most comprehensive sampling of Galium to date. A total of 194 species and variations (subspecies) of Galium were sampled to determine phylogenetic relationships, using two nuclear and five chloroplast markers. Our data are largely consistent with all previous phylogenetic results and confirmed that Galium is non-monophyletic, as are most of its sections. Most members of Galium, including the Chinese taxa, fall into three large clades mixed with other genera from the Galium s.l. group; the exception being the distinct Galium paradoxum Maxim., the first diverged lineage in the Galium s.l. group, which was treated as a new genus (Pseudogalium L.-E. Yang, Z.-L. Nie & H. Sun, gen. nov.). The Galium s.s is a well-supported clade comprised entirely of Galium species, usually with six or more leaves per whorl, mostly from the Old World. Samples from G. maximowiczii (Kom.) Pobed, G. sect. Depauperata and sect. Aparinoides, together with a few from Asperula sect. Glabella and Microphysa (Schrenk ex Fisch. & C.A. Mey.) Pobed., form the second clade. The third clade comprises taxa purely from Galium that usually have four leaves per whorl, from both the New and Old World. Our results also indicated that the monotypic genus Microphysa should be retained and clarified phylogenetic relationships of some specific confused taxa from China. Unlike prior inferences, the combination of opposite leaves associated with two stipules is proposed as the ancestral characteristic of the Galium s.l. group and even the tribe. In addition, the shapes of different corolla and inflorescence types are important for distinguishing some taxa within Rubieae.
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http://dx.doi.org/10.1016/j.ympev.2018.04.004DOI Listing
September 2018

Role of the Qinghai-Tibetan Plateau uplift in the Northern Hemisphere disjunction: evidence from two herbaceous genera of Rubiaceae.

Sci Rep 2017 10 17;7(1):13411. Epub 2017 Oct 17.

Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China.

To assess the role of the Qinghai-Tibetan Plateau uplift in shaping the intercontinental disjunction in Northern Hemisphere, we analyzed the origin and diversification within a geological timeframe for two relict herbaceous genera, Theligonum and Kelloggia (Rubiaceae). Phylogenetic relationships within and between Theligonum and Kelloggia as well as their relatives were inferred using five chloroplast markers with parsimony, Bayesian and maximum-likelihood approaches. Migration routes and evolution of these taxa were reconstructed using Bayesian relaxed molecular clock and ancestral area reconstruction. Our results suggest the monophyly of each Theligonum and Kelloggia. Eastern Asian and North American species of Kelloggia diverged at ca.18.52 Mya and the Mediterranean species of Theligonum diverged from eastern Asian taxa at ca.13.73 Mya. Both Kelloggia and Theligonum are Tethyan flora relicts, and their ancestors might have been occurred in warm tropical to subtropical environments along the Tethys coast. The Qinghai-Tibetan Plateau separated the eastern and western Tethyan area may contribute significantly to the disjunct distributions of Theligonum, and the North Atlantic migration appears to be the most likely pathway of expansion of Kelloggia to North America. Our results highlight the importance role of the QTP uplift together with corresponding geological and climatic events in shaping biodiversity and biogeographic distribution in the Northern Hemisphere.
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http://dx.doi.org/10.1038/s41598-017-13543-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645396PMC
October 2017

The Biogeographic South-North Divide of Polygonatum (Asparagaceae Tribe Polygonateae) within Eastern Asia and Its Recent Dispersals in the Northern Hemisphere.

PLoS One 2016 3;11(11):e0166134. Epub 2016 Nov 3.

Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China.

Eastern Asia (EA) is a key region for the diversification of flowering plants in the Northern Hemisphere, but few studies have focused on the biogeographic history within EA in the context of the other northern continents. Polygonatum is an important medicinal genus widely distributed in the Northern Hemisphere with its highest species richness in EA, and it represents an excellent model for studying the evolution of biogeographic patterns in this region. Divergence time estimation was used to examine the biogeographic history of Polygonatum based on nuclear ITS and four plastid sequences (rbcL, matK, psbA-trnH and trnC-petN) from 30 Polygonatum species and 35 outgroup taxa. The ancestral area of Polygonatum and subsequent dispersal routes were inferred using Bayes-Lagrange. Polygonatum was estimated to have originated in southern EA during the middle Miocene (14.34-13.57 Ma) with subsequent south-to-north expansion in the late Miocene. Multiple intercontinental dispersal events were inferred between EA and Europe or North America, and all of them have occurred recently in the late Miocene to Pliocene. The separation of Polygonatum into the south and north lineages and their subsequent diversifications in the late Miocene supports the existence of a biogeographic divide between the northern and southern parts of EA that also coincides with the retreat and redevelopment of the arid zone in EA in the Neogene. Our results demonstrate the complexity of biogeographic history of Polygonatum in the Northern Hemisphere including early vicariance followed by frequent and recent dispersals in the Neogene.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166134PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094755PMC
June 2017

Molecular Phylogeny of Gueldenstaedtia and Tibetia (Fabaceae) and Their Biogeographic Differentiation within Eastern Asia.

PLoS One 2016 15;11(9):e0162982. Epub 2016 Sep 15.

Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China.

Tibetia and Gueldenstaedtia are two morphologically similar and small genera in Fabaceae, with distributions largely corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms in eastern Asia, respectively. These two genera have confusing relationships based on morphology; therefore, we aimed to provide a clear understanding of their phylogenetic and biogeographic evolution within eastern Asia. In our investigations we included 88 samples representing five Gueldenstaedtia species, five Tibetia species, and outgroup species were sequenced using five markers (nuclear: ITS; chloroplast: matK, trnL-F, psbA-trnH and rbcL). Our phylogenetic results support (1) the monophyly of Tibetia and of Gueldenstaedtia, respectively; and (2) that Tibetia and Gueldenstaedtia are sister genera. Additionally, our data identified that Tibetia species had much higher sequence variation than Gueldenstaedtia species. Our results suggest that the two genera were separated from each other about 17.23 million years ago, which is congruent with the Himalayan orogeny and the uplift of the Tibetan Plateau in the mid Miocene. The divergence of Tibetia and Gueldenstaedtia is strongly supported by the separation of the Sino-Himalayan and Sino-Japanese region within eastern Asia. In addition, the habitat heterogeneity may accelerate the molecular divergence of Tibetia in the Sino-Himalayan region.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162982PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025100PMC
August 2017

Climatic Factors Drive Population Divergence and Demography: Insights Based on the Phylogeography of a Riparian Plant Species Endemic to the Hengduan Mountains and Adjacent Regions.

PLoS One 2015 21;10(12):e0145014. Epub 2015 Dec 21.

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.

Quaternary climatic factors have played a significant role in population divergence and demography. Here we investigated the phylogeography of Osteomeles schwerinae, a dominant riparian plant species of the hot/warm-dry river valleys of the Hengduan Mountains (HDM), Qinling Mountains (QLM) and Yunnan-Guizhou Plateau (YGP). Three chloroplast DNA (cpDNA) regions (trnD-trnT, psbD-trnT, petL-psbE), one single copy nuclear gene (glyceraldehyde 3-phosphate dehydrogenase; G3pdh), and climatic data during the Last Interglacial (LIG; c. 120-140 ka), Last Glacial Maximum (LGM; c. 21 ka), and Current (c. 1950-2000) periods were used in this study. Six cpDNA haplotypes and 15 nuclear DNA (nDNA) haplotypes were identified in the 40 populations of O. schwerinae. Spatial Analysis of Molecular Variance, median-joining networks, and Bayesian phylogenetic trees based on the cpDNA and nDNA datasets, all suggested population divergence between the QLM and HDM-YGP regions. Our climatic analysis identified significant heterogeneity of the climatic factors in the QLM and HDM-YGP regions during the aforementioned three periods. The divergence times based on cpDNA and nDNA haplotypes were estimated to be 466.4-159.4 ka and 315.8-160.3 ka, respectively, which coincide with the time of the weakening of the Asian monsoons in these regions. In addition, unimodal pairwise mismatch distribution curves, expansion times, and Ecological Niche Modeling suggested a history of population expansion (rather than contraction) during the last glaciation. Interestingly, the expansion times were found being well consistent with the intensification of the Asian monsoons during this period. We inferred that the divergence between the two main lineages is probably caused by disruption of more continuous distribution because of weakening of monsoons/less precipitation, whilst subsequent intensification of the Asian monsoons during the last glaciation facilitated the expansion of O. schwerinae populations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145014PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687034PMC
June 2016

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

Mol Phylogenet Evol 2016 Feb 3;95:217-28. Epub 2015 Nov 3.

Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA. Electronic address:

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 (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). 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.
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http://dx.doi.org/10.1016/j.ympev.2015.10.013DOI Listing
February 2016

Recent assembly of the global herbaceous flora: evidence from the paper daisies (Asteraceae: Gnaphalieae).

New Phytol 2016 Mar 3;209(4):1795-806. Epub 2015 Nov 3.

Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA.

The global flora is thought to contain a large proportion of herbs, and understanding the general spatiotemporal processes that shaped the global distribution of these communities is one of the most difficult issues in biogeography. We explored patterns of world-wide biogeography in a species-rich herbaceous group, the paper daisy tribe Gnaphalieae (Asteraceae), based on the hitherto largest taxon sampling, a total of 835 terminal accessions representing 80% of the genera, and encompassing the global geographic range of the tribe, with nuclear internal transcribed spacer (ITS) and external transcribed spacer (ETS) sequences. Biogeographic analyses indicate that Gnaphalieae originated in southern Africa during the Oligocene, followed by repeated migrations into the rest of Africa and the Mediterranean region, with subsequent entries into other continents during various periods starting in the Miocene. Expansions in the late Miocene to Pliocene appear to have been the driving force that shaped the global distribution of the tribe as forests were progressively broken up by the mid-continent aridification and savannas and grasslands expanded into the interior of the major continents. This pattern of recent colonizations may explain the world-wide distribution of many other organisms in open ecosystems and it is highlighted here as an emerging pattern in the evolution of the global flora.
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http://dx.doi.org/10.1111/nph.13740DOI Listing
March 2016

Systematics, biogeography, and character evolution of Deutzia (Hydrangeaceae) inferred from nuclear and chloroplast DNA sequences.

Mol Phylogenet Evol 2015 Jun 14;87:91-104. Epub 2015 Mar 14.

Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, Yunnan, PR China. Electronic address:

The genus Deutzia (Hydrangeaceae), containing ca. 60 species circumscribed in three sections, is disjunctly distributed in eastern Asia and Central America (Mexico). Although the genus is well delimited, its subdivisions into sections and series have not been the subject of an explicit test of monophyly based on molecular data. A comprehensive examination of the evolutionary relationships within the genus is thus still lacking. We present a fossil-calibrated, molecular phylogeny of Deutzia based on two nuclear ribosomal DNA (ITS and 26S) and three chloroplast DNA regions (matK, rbcL, and trnL-F intergenic spacer). Within this framework, we examine character evolution in petal arrangement, filament shape, and the number of stamens, and infer the ancestral area and biogeographic history of the genus. Our molecular phylogeny suggests that Deutzia is monophyletic. Two major clades are recovered: one composed of the species of sect. Neodeutzia from Mexico, and the other containing all remaining Deutzia species of sections Mesodeutzia and Deutzia from SW China and Northeast Asia. The latter two Asian sections were each revealed to be polyphyletic. The induplicate petals, 2-dentate filaments, and polystemonous androecia are inferred to be ancestral character states. Biogeographic reconstructions suggest a Northeast Asian origin for the genus and subsequent spread to Mexico during the Oligocene and to SW China during the Miocene. Based on our results, a new infrageneric classification of Deutzia inferred from molecular phylogeny is required. We propose to merge sections Mesodeutzia and Deutzia to ensure the monophyly at the sectional level. Cooling trends during the Oligocene resulted in isolation, separating eastern Asian and Mexican taxa, while the warm period during the middle Miocene stimulated the diversification from Northeast Asia to SW China. The uplift in the Qinghai-Tibetan Plateau and monsoon regimes are important in promoting high species diversification of Deutzia in SW China.
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http://dx.doi.org/10.1016/j.ympev.2015.03.002DOI Listing
June 2015

Molecular phylogeny and biogeographic diversification of linnaeoideae (caprifoliaceae s. L.) disjunctly distributed in Eurasia, North America and Mexico.

PLoS One 2015 10;10(3):e0116485. Epub 2015 Mar 10.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.

Linnaeoideae is a small subfamily of erect or creeping shrubs to small trees in Caprifoliaceae that exhibits a wide disjunct distribution in Eurasia, North America and Mexico. Most taxa of the subfamily occur in eastern Asia and Mexico but the monospecific genus Linnaea has a circumboreal to north temperate distribution. In this study, we conducted phylogenetic and biogeographic analyses for Linnaeoideae and its close relatives based on sequences of the nuclear ribosomal ITS and nine plastid (rbcL, trnS-G, matK, trnL-F, ndhA, trnD-psbM, petB-D, trnL-rpl32 and trnH-psbA) markers. Our results support that Linnaeoideae is monophyletic, consisting of four eastern Asian lineages (Abelia, Diabelia, Dipelta and Kolkwitzia), the Mexican Vesalea, and Linnaea. The Mexican Vesalea was formerly placed in Abelia, but it did not form a clade with the eastern Asian Abelia; instead Vesalea and Linnaea are sisters. The divergence time between the eastern Asian lineages and the Mexican Vesalea plus the Linnaea clade was dated to be 50.86 Ma, with a 95% highest posterior density of 42.8 Ma (middle Eocene) to 60.19 Ma (early Paleocene) using the Bayesian relaxed clock estimation. Reconstructed ancestral areas indicated that the common ancestor of Linnaea plus Vesalea may have been widespread in eastern Asia and Mexico or originated in eastern Asia during the Eocene and likely migrated across continents in the Northern Hemisphere via the North Atlantic Land Bridges or the Bering Land Bridge. The Qinling Mountains of eastern Asia are the modern-day center of diversity of Kolkwitzia-Dipelta-Diabelia clade. The Diabeliaclade became highly diversified in Japan and eastern China. Populations of Diabelia serrata in Japan and eastern China were found to be genetically identical in this study, suggesting a recent disjunction across the East China Sea, following the last glacial event.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116485PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355296PMC
January 2016

Does the Arcto-Tertiary biogeographic hypothesis explain the disjunct distribution of Northern Hemisphere herbaceous plants? The case of Meehania (Lamiaceae).

PLoS One 2015 6;10(2):e0117171. Epub 2015 Feb 6.

Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan, China.

Despite considerable progress, many details regarding the evolution of the Arcto-Tertiary flora, including the timing, direction, and relative importance of migration routes in the evolution of woody and herbaceous taxa of the Northern Hemisphere, remain poorly understood. Meehania (Lamiaceae) comprises seven species and five subspecies of annual or perennial herbs, and is one of the few Lamiaceae genera known to have an exclusively disjunct distribution between eastern Asia and eastern North America. We analyzed the phylogeny and biogeographical history of Meehania to explore how the Arcto-Tertiary biogeographic hypothesis and two possible migration routes explain the disjunct distribution of Northern Hemisphere herbaceous plants. Parsimony and Bayesian inference were used for phylogenetic analyses based on five plastid sequences (rbcL, rps16, rpl32-trnH, psbA-trnH, and trnL-F) and two nuclear (ITS and ETS) gene regions. Divergence times and biogeographic inferences were performed using Bayesian methods as implemented in BEAST and S-DIVA, respectively. Analyses including 11 of the 12 known Meehania taxa revealed incongruence between the chloroplast and nuclear trees, particularly in the positions of Glechoma and Meehania cordata, possibly indicating allopolyploidy with chloroplast capture in the late Miocene. Based on nrDNA, Meehania is monophyletic, and the North American species M. cordata is sister to a clade containing the eastern Asian species. The divergence time between the North American M. cordata and the eastern Asian species occurred about 9.81 Mya according to the Bayesian relaxed clock methods applied to the combined nuclear data. Biogeographic analyses suggest a primary role of the Arcto-Tertiary flora in the study taxa distribution, with a northeast Asian origin of Meehania. Our results suggest an Arcto-Tertiary origin of Meehania, with its present distribution most probably being a result of vicariance and southward migrations of populations during climatic oscillations in the middle Miocene with subsequent migration into eastern North America via the Bering land bridge in the late Miocene.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117171PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319762PMC
January 2016

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 2014 16(42):11-9. Epub 2014 Sep 16.

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China ; Key Laboratory of Plant Resources Conservation and Utilization and College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China.

The genus Nekemias (Vitaceae) was first recognized by Rafinesque in 1838. It has been treated as a synonym of Ampelopsis Michx. Recent phylogenetic studies suggest that Ampelopsis as traditionally delimited is paraphyletic. To maintain the monophyly of each of the genera of Vitaceae, we herein segregate the Ampelopsissect.Leeaceifoliae lineage from Ampelopsis and recognize these taxa in Nekemias Raf., which has a disjunct distribution in eastern to southeastern Asia and eastern North America. Nomenclatural changes are made for nine species and one variety: Nekemiasarborea (L.) J. Wen & Boggan, Nekemiascantoniensis (Hook. & Arn.) J. Wen & Z.L. Nie, Nekemiascelebica (Suess.) J. Wen & Boggan, Nekemiaschaffanjonii (H. Lév. & Van.) J. Wen & Z.L. Nie, Nekemiasgongshanensis (C.L. Li) J. Wen & Z.L. Nie, Nekemiasgrossedentata (Hand.-Mazz.) J. Wen & Z.L. Nie, Nekemiashypoglauca (Hance) J. Wen & Z.L. Nie, Nekemiasmegalophylla (Diels & Gilg) J. Wen & Z.L. Nie, Nekemiasmegalophyllavar.jiangxiensis (W.T. Wang) J. Wen & Z.L. Nie, and Nekemiasrubifolia (Wall.) J. Wen & Z.L. Nie. A taxonomic key is provided for the genus to facilitate identification.
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http://dx.doi.org/10.3897/phytokeys.42.7704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223361PMC
November 2014

Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau.

Front Genet 2014 12;5. Epub 2014 Feb 12.

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China.

The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences, pollinator-mediated isolation, diploid hybridization and introgression, and allopolyploidy. These mechanisms have driven spectacular radiations and/or species diversifications in various groups of plants such as Pedicularis L., Saussurea DC., Rhododendron L., Primula L., Meconopsis Vig., Rhodiola L., and many lineages of gymnosperms. Nevertheless, much work is needed toward understanding the evolutionary mechanisms of plant diversifications on the QTP. Well-sampled biogeographic analyses of the QTP plants in the broad framework of the Northern Hemisphere as well as the Southern Hemisphere are still relatively few and should be encouraged in the next decade. This paper reviews recent evidence from phylogenetic and biogeographic studies in plants, in the context of rapid radiations, mechanisms of species diversifications on the QTP, and the biogeographic significance of the QTP in the broader context of both the Northern and Southern Hemisphere biogeography. Integrative multidimensional analyses of phylogeny, morphological innovations, geography, ecology, development, species interactions and diversifications, and geology are needed and should shed insights into the patterns of evolutionary assembly and radiations in this fascinating region.
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http://dx.doi.org/10.3389/fgene.2014.00004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921583PMC
June 2014

Transcriptome sequences resolve deep relationships of the grape family.

PLoS One 2013 17;8(9):e74394. Epub 2013 Sep 17.

Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C., United States of America.

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074394PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775763PMC
May 2014

Phylogeography of Sophora davidii (Leguminosae) across the 'Tanaka-Kaiyong Line', an important phytogeographic boundary in Southwest China.

Mol Ecol 2013 Aug;22(16):4270-4288

Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China.

The 'Tanaka-Kaiyong Line' (TKL) is a major phytogeographic boundary in Southwest China, separating East Asia's Sino-Himalayan and Sino-Japanese Floras. However, little is known about the importance of this boundary in promoting intraspecific phylogeographic subdivision and divergence. Using chloroplast (cpDNA) and nuclear-intron (nDNA) sequence data, we reconstructed the population history of Sophora davidii, a drought-tolerant riparian shrub widely distributed on either side of the TKL. Specifically, we aimed at testing two long-standing explanations for possible vicariant events across the TKL: (i) Late Pliocene (c. 3 Ma) geological uplift of the eastern Qinghai-Tibetan Plateau (QTP) or (ii) a sharp environmental gradient associated with the establishment of different monsoon regimes on either side of the TKL during the (Late) Pleistocene. Our genealogical analyses detected a major west-east split in cpDNA, geographically largely consistent with the TKL, and dated to c. 1.28 Ma (95% HPD: 0.21-2.96 Ma), hence postdating the latest phase of eastern QTP uplift. Furthermore, integrating cpDNA phylogeographic patterns with mismatch analyses, we found multiple refugial isolation and long-term demographic stability of populations in the west (Hengduan Mountain Range) compared with extensive range expansions in the east, possibly during the last glacial period(s) and followed by differentiation into regional sublineages (southeast: Yunnan-Guizhou Plateau vs. northeast: Qinling Mts./Loess Plateau). Although nuclear differentiation was less marked, the geographical pattern of nDNA haplotypes provided some further indication of the species' eastward expansion, possibly from source populations located just east of the TKL (lower Jinshajiang region). Overall, the present data reject the geological (tectonic) explanation for the TKL and, instead, provide supportive evidence for its role as a climatically driven barrier to present-day plant dispersal. In addition, our study highlights changing temperatures and vegetation types during the last glacial period(s), along with aspects of regional topography, to be important determinants of the glacial eastward expansion of S. davidii. In consequence, our study lends support to a 'glacial out-of-Hengduan Mts'. hypothesis for the xerophytic-riparian flora of Southwest China, which in turn is inconsistent with the traditional view of the TKL as a 'classical' vicariant-biogeographic boundary.
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http://dx.doi.org/10.1111/mec.12388DOI Listing
August 2013

Post-Boreotropical dispersals explain the pantropical disjunction in Paederia (Rubiaceae).

Ann Bot 2013 May 10;111(5):873-86. Epub 2013 Mar 10.

Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.

Background And Aims: Pantropical intercontinental disjunction is a common biogeographical pattern in flowering plants exhibiting a discontinuous distribution primarily in tropical Asia, Africa and the Americas. Only a few plant groups with this pattern have been investigated at the generic level with molecular phylogenetic and biogeographical methods. Paederia (Rubiaceae) is a pantropical genus of 31 species of woody lianas, with the greatest species diversity in continental Asia and Madagascar and only two species from tropical America. The aim of this study was to reconstruct the biogeographical history of Paederia based on phylogenetic analyses to explore how the genus attained its pantropical distribution.

Methods: Maximum parsimony and Bayesian inference were used for phylogenetic analyses using sequences of five plastid markers (the rbcL gene, rps16 intron, trnT-F region, atpB-rbcL spacer and psbA-trnH spacer). Biogeographical inferences were based on a Bayesian uncorrelated lognormal relaxed molecular clock together with both Bayesian and likelihood ancestral area reconstructions.

Key Results: The data suggest an early diverged Asian lineage sister to the clade of the remaining species consisting of a predominantly Asian sub-clade and a primarily Malagasy sub-clade. Paederia is inferred to have originated in the Oligocene in tropical continental Asia. It then reached Africa in the early to middle Miocene, most probably via long-distance dispersal across the Indian Ocean. The two Neotropical species are inferred to have derived independently in the late Miocene from ancestors of Asia and East Africa, respectively.

Conclusions: The results demonstrate the importance of post-Boreotropical long-distance dispersals (across three major oceans) in shaping the global pantropical disjunction in some plants, such as Paederia, with small, winged diaspores adapted to long-distance dispersal by various agents including wind, ocean currents or birds. Overland migration is less likely to explain its palaeotropical disjunction between Asia and Africa.
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http://dx.doi.org/10.1093/aob/mct053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631337PMC
May 2013

Polyphyly of the Padus group of Prunus (Rosaceae) and the evolution of biogeographic disjunctions between eastern Asia and eastern North America.

J Plant Res 2013 May 14;126(3):351-61. Epub 2012 Dec 14.

College of Life Science, Northwest Agriculture and Forest University, Yangling, Shaanxi, China.

Prunus subgenus Padus is a group with a wide distribution in temperate eastern Asia and eastern North America with one species extending to Europe and one to Central America. Phylogenetic relationships of subgenus Padus were reconstructed using sequences of nuclear ribosomal ITS, and plastid ndhF gene, and rps16 intron and rpl16 intron. Prunus subgenus Padus is shown to be polyphyletic. Taxa of subgenus Padus and subgenus Laurocerasus are highly intermixed in both the ITS and the plastid trees. The results support two disjunctions between eastern North America and Eurasia within the Padus group. One disjunction is between Prunus virginiana of eastern North America and P. padus of Eurasia, estimated to have diverged at 2.99 (95 % HPD 0.59-6.15)-4.1 (95 % HPD 0.63-8.59) mya. The other disjunction is between P. serotina and its Asian relatives. The second disjunction may have occurred earlier than the former one, but the age estimate is difficult due to the unresolved phylogenetic position of the P. serotina complex.
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http://dx.doi.org/10.1007/s10265-012-0535-1DOI Listing
May 2013

Molecular phylogeny of Anaphalis (Asteraceae, Gnaphalieae) with biogeographic implications in the Northern Hemisphere.

J Plant Res 2013 Jan 10;126(1):17-32. Epub 2012 Jul 10.

Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 132# Lanhei Road, Kunming 650201, Yunnan, China.

Anaphalis is the largest Asian genus in the tribe Gnaphalieae (Asteraceae) and has its greatest species diversity in the eastern Himalayas. The nuclear internal and external transcribed spacers were sequenced for Anaphalis species, with an emphasis on the eastern Himalayan taxa to examine the monophyly and construct the phylogenetic relationships of and within the genus. The results suggest that all species of Anaphalis are nested with Helichrysum, showing a close relationship with a Mediterranean-Asian group of Helichrysum. Although the monophyly of Anaphalis is only weakly supported, two clades within the genus are well recognized, each consisting of two subgroups. The inferred phylogenetic relationships within Anaphalis correspond to the shape of leaf base, rather than the morphology of the capitula and phyllaries that are usually used for species delimitation and classification in the genus. All four subgroups of Anaphalis are common and diversified in the eastern Himalayas with multiple dispersals out of this region. The sole North American species of Anaphalis is best hypothesized to be the result of long-distance dispersal or overland migration via Bering land bridge from Asia. Our analyses suggest that the extant distribution of Anaphalis has most likely resulted one radiation into the eastern Himalayas followed by repeated independent dispersals and/or radiations mostly into eastern Asia but also into the western Himalayas, North America, and southeast Asia.
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http://dx.doi.org/10.1007/s10265-012-0506-6DOI Listing
January 2013

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

BMC Evol Biol 2012 Feb 8;12:17. Epub 2012 Feb 8.

Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China.

Background: 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.

Results: 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).

Conclusions: 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.
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http://dx.doi.org/10.1186/1471-2148-12-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299610PMC
February 2012

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

Am J Bot 2010 Aug 14;97(8):1342-53. Epub 2010 Jul 14.

Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, P. R. China.

Unlabelled:

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.
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http://dx.doi.org/10.3732/ajb.1000085DOI Listing
August 2010

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

Mol Phylogenet Evol 2008 Nov 3;49(2):424-34. Epub 2008 Aug 3.

Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Kunming, Yunnan 650204, PR China.

Maianthemum (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 relying 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.
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http://dx.doi.org/10.1016/j.ympev.2008.07.017DOI Listing
November 2008

Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets.

Mol Phylogenet Evol 2008 Sep 21;48(3):1027-40. Epub 2008 Jun 21.

Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, PR China.

This study employs three nuclear genes (PHYA, LFY, and GAI1) to reconstruct the phylogenetic and biogeographic history of Magnoliaceae. A total of 104 samples representing 86 taxa from all sections and most subsections were sequenced. Twelve major groups are well supported to be monophyletic within Magnoliaceae and these groups are largely consistent with the recent taxonomic revision at the sectional and subsectional levels. However, relationships at deeper nodes of the subfamily Magnolioideae remain not well resolved. A relaxed clock relying on uncorrelated rates suggests that the complicated divergent evolution of Magnolioideae began around the early Eocene (54.57mya), concordant with paleoclimatic and fossil evidence. Intercontinental disjunctions of Magnoliaceae in the Northern Hemisphere appear to have originated during at least two geologic periods. Some occurred after the middle Miocene, represented by two well-recognized temperate lineages disjunct between eastern Asia and eastern North America. The others may have occurred no later than the Oligocene, with ancient separations between or within tropical and temperate lineages.
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http://dx.doi.org/10.1016/j.ympev.2008.06.004DOI Listing
September 2008

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

Am J Bot 2006 Sep;93(9):1343-56

Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China;

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) 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.
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http://dx.doi.org/10.3732/ajb.93.9.1343DOI Listing
September 2006
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