Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae)

The genus Lespedeza (Fabaceae) consists of 40 species disjunctively distributed in East Asia and eastern North America. Phylogenetic relationships of all Lespedeza species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses of sequence data from five chloroplast (rpl16, rpl32-trnL, rps16-trnQ, trnL-F, and trnK/matK) and one nuclear (ITS) DNA regions. All analyses yielded consistent relationships among major lineages. Our results suggested that Campylotropis, Kummerowia, and Lespedeza are monophyletic, respectively. Lespedeza is resolved as sister to Kummerowia and these two together are further sister to Campylotropis. Neither of the two subgenera, subgen. Lespedeza and subgen. Macrolespedeza, in Lespedeza based on morphological characters, is recovered as monophyletic. Within Lespedeza, the North American clade is retrieved as sister to the Asian clade. The nuclear and chloroplast markers showed incongruent phylogenetic signals at shallow-level phylogeny, which may point to either introgression or incomplete lineage sorting in Lespedeza. The divergence times within Lespedeza and among related genera were estimated using Bayesian approach with BEAST. It is assumed that following the divergence between Kummerowia and Lespedeza in Asia in the late Miocene, the ancestor of Lespedeza diverged into the North American and the Asian lineages. The North American ancestor quickly migrated to North America through the Bering land bridge in the late Miocene. The North American and Asian lineages started to diversify almost simultaneously in the late Miocene but resulted in biased numbers of species in two continents.     

Phylogeographic history of the woodwardioid ferns,including species from the Himalayas

The woodwardioid ferns are well-represented in the Northern Hemisphere, where they are disjunctly distributed throughout the warm temperate and subtropical regions of North America, Europe, and Asia. To infer the biogeographic history of the woodwardioid ferns, the phylogeny of Woodwardia was estimated using rbcL and rps4 sequences from divergent distribution regions including the Himalayas. Phylogenetic results support Woodwardia as a monophyletic group with Woodwardia areolatae and W. virginica as basal, these two species from eastern North America diverged early, which are sister clades to the remaining species from America, Europe, and Asia. Based on analyses of the fossil records of these species for divergence times, Woodwardia species were estimated to have diverged initially in the Paleogene of North America. After its New World origin, a greater diversification and expansion of Woodwardia occurred in eastern Eurasia, with the European arrival of Woodwardia radicans during the Middle Miocene. Compared to earlier reports, a migration back into North America via the Bering land bridge is consistent with these data.     

Does the Arcto-Tertiary Biogeographic Hypothesis Explain the Disjunct Distribution of Northern Hemisphere Herbaceous Plants? The Case of Meehania (Lamiaceae)

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.     

Molecular systematics and biogeography of Wisteria inferred from nucleotide sequences of nuclear and plastid genes

Previous molecular phylogenetic studies of Fabaceae indicated that species of Wisteria, an intercontinental disjunct genus between eastern Asia and eastern North America, formed a clade derived from within Callerya. However, interspecific relationships were not well resolved or supported. In this study, we used sequences of the nuclear ribosomal DNA internal transcribed spacer region and the chloroplast gene matK to examine interspecific relationships and explore implications of the phylogeny for the systematics and biogeography of Wisteria. Our results showed that Wisteria with deciduous leaves and racemose inflorescences formed a strongly supported clade derived from within the paraphyletic Callerya. Afgekia was also found to be included within Callerya. Therefore, our data support the merger ofAfgekia, Callerya, and Wisteria. The phylogenetic pattern suggested that the deciduousness in Wisteria may be a derived trait likely in response to temperate climate, and the racemose inflorescences in the Afgekia–Callerya–Wisteria clade may have evolved from panicles. Our study also provided strong support for the sister relationship of the North American and eastern Asian species of Wisteria. In the Asian clade, Wisteria brachybotrys Siebold & Zucc. of Japan was sister to the clade containing W. floribunda (Willd.) DC of Japan and Korea, and W. sinensis (Sims) Sweet of China. However, our data offered weak support for the sister relationship ofW. floribunda and W. sinensis. Our divergence time and biogeographic analyses suggested that the eastern Asian–North American disjunction in Wisteria may have occurred through a dispersal event in the middle Miocene (13.4 Mya) from the Old World to the New World across the Bering land bridge followed by vicariance in the late Miocene (6.8 Mya). This study added another example to the “out of Asia” migration for the eastern Asian–eastern North American disjunction.     

Chloroplast phylogenomics of the New World grape species (Vitis,Vitaceae)

Vitis L. (the grape genus) is the economically most important fruit crop, as the source of grapes and wine. Phylogenetic relationships within the genus have been highly controversial. Herein, we employ sequence data from whole plastomes to attempt to enhance Vitis phylogenetic resolution. The results support the New World Vitis subgenus Vitis as monophyletic. Within the clade, V. californica is sister to the remaining New World Vitis subgenus Vitis. Furthermore, within subgenus Vitis, a Eurasian clade is robustly supported and is sister to the New World clade. The clade of Vitis vinifera ssp. vinifera and V. vinifera ssp. sylvestris is sister to the core Asian clade of Vitis. Several widespread species in North America are found to be non‐monophyletic in the plastome tree, for example, the broadly defined Vitis cinerea and V. aestivalis each needs to be split into several species. The non‐monophyly of some species may also be due to common occurrences of hybridizations in North American Vitis. The classification of North American Vitis by Munson into nine series is discussed based on the phylogenetic results. Analyses of divergence times and lineage diversification support a rapid radiation of Vitis in North America beginning in the Neogene.     

ISOZYME DIVERGENCE BETWEEN EASTERN ASIAN,NORTH AMERICAN,AND TURKISH SPECIES OF LIQUIDAMBAR (HAMAMELIDACEAE)

The deciduous woody genus Liquidambar has four morphologically similar species in eastern and western Asia, eastern North America, and Central America. Liquidambar styraciflua is found in the eastern United States and Central America, L. orientalis is native only to southwest Turkey, and L. formosana and L. acalycina occur in eastern Asia. This genus is one of many that contributes to the floristic similarities observed between these different regions. Allelic variation was scored at 22 isozyme loci from 41 populations. The level of genetic divergence between species on different continents is high. Nei's genetic identity was 0.431 between L. formosana and L. styraciflua, 0.485 between L. acalycina and L. styraciflua, 0.512 between L. orientalis and L. styraciflua, 0.256 between L. formosana and L. orientalis, and 0.305 between L. acalycina and L. orientalis. Estimates of time of divergence from the isozyme data suggest that the current species diverged before or during the Miocene. The pattern of relationships portrayed by the isozyme data suggest a longer period of separation between the eastern and western Asian forms of this genus. In addition, the eastern North American and Turkish species appear to be the most closely related intercontinental pair of species providing evidence for a North Atlantic land bridge as late as the Miocene. It would appear, therefore, that the North American populations were in contact with the Asian populations over the North Pacific and North Atlantic possibly as late as the Miocene, but that the separation between the two Asian populations occurred much earlier. The time of divergence as measured from the isozyme data correlates with an independent assessment of the origin of these disjuncts as determined from the fossil record.     

Evolution of the Eastern Asian and Eastern North American disjunct genus Symplocarpus (Araceae): insights from chloroplast DNA restriction site data

Chloroplast DNA (cpDNA) variation was surveyed with 20 restriction endonucleases for the eastern Asian and eastern North American disjunct genus Symplocarpus (Araceae). The cpDNA phylogeny reveals a sister group relationship between S. foetidus from eastern North America and S. renifolius from eastern Asia. The cpDNA divergence between the two intercontinental sister species is 0.61%, which suggests an estimated divergence time of 6.1 million years ago during the late Miocene. The Bering land bridge hypothesis is compatible with the estimated time of divergence for the migration of Symplocarpus between eastern Asia and North America. Furthermore, a single origin of the exothermic spadices in Symplocarpus is suggested by the phylogeny. The cpDNA data also provide independent support for the recognition of three species within the genus.     

Biogeography of North Pacific <Emphasis Type="Italic">Isoëtes</Emphasis> (Isoëtaceae) inferred from nuclear and chloroplast DNA sequence data

Recent advances in phylogenetics indicate that reticulate evolution has played an important role in the emergence of Isoëtes species in the North Pacific region. However, the biogeographical origin of the North Pacific Isoëtes species remains contentious. We present a fossilcalibrated phylogeny of species from the North Pacific region based on molecular data. Within this framework, we discuss their ancestral areas and biogeographical history. North Pacific Isoëtes are divided into two clades: clade I, consisting of East Asian, Papua New Guinean, and Australian species, and clade II, consisting of West Beringian and western North American species. Within clade I, Australian Isoëtes species were an early divergent group, and Papua New Guinea’s species form a sister clade to the East Asian species. Biogeographical reconstructions suggest an Australasian origin for the East Asian species that arose through long-distance dispersal during the late Oligocene. Within clade II, I. asiatica from West Beringia forms a clade with I. echinospora and I. muricata from Alaska. Western North America was the area of origin for the dispersal of Isoëtes species to West Beringia via the Bering land bridge during the late Miocene. Our study identifies the biogeographic origin of the North Pacific Isoëtes and suggests long-distance dispersal as the most likely explanation for their intercontinental distribution.     

Molecular phylogeny and historical biogeography of the Holarctic wetland leaf beetle of the genus Plateumaris

Leaf beetles of the genus Plateumaris inhabit wetlands across the temperate zone of the Holarctic region. To explore the phylogeographic relationships among North American, East Asian, and European members of this genus and the origin of the species endemic to Japan, we studied the molecular phylogeny of 20 of the 27 species in this genus using partial sequences of mitochondrial cytochrome oxidase subunit I (COI) and the 16S and nuclear 28S rRNA genes. The molecular phylogeny revealed that three species endemic to Europe are monophyletic and sister to the remaining 11 North American and six Asian species. Within the latter clade, North American and Asian species did not show reciprocal monophyly. Dispersal-vicariance analysis and divergence time estimation revealed that the European and North America-Asian lineages diverged during the Eocene. Moreover, subsequent differentiation occurred repeatedly between North American and Asian species, which was facilitated by three dispersal events from North America to Asia and one in the opposite direction during the late Eocene through the late Miocene. Two Japanese endemics originated from different divergence events; one differentiated from the mainland lineage after differentiation from the North American lineage, whereas the other showed a deep coalescence from the North American lineage with no present-day sister species on the East Asian mainland. This study of extant insects provides molecular phylogenetic evidence for ancient vicariance between Europe and East Asia-North America, and for more recent (but pre-Pleistocene) faunal exchanges between East Asia and North America.     

Phylogenetic assessment and biogeographic analyses of tribe <Emphasis Type="Italic">Peracarpeae</Emphasis> (Campanulaceae)

Peracarpeae is a small tribe consisting of three genera: Homocodon, Heterocodon and Peracarpa, with a disjunct distribution between eastern Asia and western North America. Homocodon is endemic to southwestern China and was previously placed in the western North American genus Heterocodon. Our phylogenetic analysis using four plastid markers (matK, atpB, rbcL and trnL-F) suggests the polyphyly of Peracarpeae. Homocodon is sister to a clade consisting of the eastern Asian Adenophora, Hanabusaya and species of Campanula from the Mediterranean region and North America, rather than forming a clade with Heterocodon. Homocodon and its Eurasia relatives are estimated to have diverged in the early Miocene (16.84 mya, 95% HPD 13.35–21.45 mya). The eastern Asian Peracarpa constitutes a clade with the North American Heterocodon, Githopsis and three species of Campanula, supporting a disjunction between eastern Asia and North America in Campanulaceae. The Asian-North American disjunct lineages diverged in the early Miocene (16.17 mya, 95% HPD 13.12–20.9 mya). The biogeographic analyses suggest that Homocodon may be a relict of an early radiation in eastern Asia, and that Peracarpa and its closest North American relatives most likely originated from a Eurasian ancestor.     

Phylogeny and Phytogeography of Eupatorium (Eupatorieae, Asteraceae): Insights from Sequence Data of the nrDNA ITS Regions and cpDNA RFLP

Eupatorium were examined by sequencing the internal transcribed spacers (ITS) of nuclear ribosomal DNA and restriction site analysis of chloroplast DNA. Molecular data provided strong evidence that (1) this genus originated in North America, (2) the genus diverged into three morphological species groups, Eutrochium, Traganthes and Uncasia in North America, and (3) one of the North American Uncasia lineages migrated into temperate Europe and eastern Asia over the Bering land bridge. The estimated divergence times support a late Miocene to early Pliocene migration from North America to Eurasia via the Bering land bridge. A European species was sister to all of the eastern Asian species examined. The disjunct distribution pattern of the genus Eupatorium is incongruent with the classical Arcto-Tertiary geoflora concept. Received 13 September 1999/ Accepted in revised form 4 January 2000     

Phylogenomics and biogeography of Wisteria: Implications on plastome evolution among inverted repeat-lacking clade (IRLC) legumes

The genus Wisteria (Fabaceae) is disjunctly distributed in eastern Asian and eastern North American temperate deciduous forests, and it is widely cultivated around the world as spectacular garden plants. It is a member of inverted repeat-lacking clade (IRLC). The IRLC Species are characterized by the loss of an IR region in their plastomes, which has long been of great interest. In this research, we report whole plastome sequences from all four Wisteria species and a Wisteriopsis japonica, combining these with existing data to explore phylogenetic relationships and biogeography of Wisteria, as well as plastome evolution of IRLC species. Phylogenetic analyses recognized a clade containing Glycyrrhiza–Wisteriopsis–Wisteria as sister to the remaining genera of IRLC. North American Wisteria frutescens and the three Asian species formed reciprocal clades, and Wisteria brachybotrys was sister to Wisteria floribunda and Wisteria sinensis. Wisteria may have originated in Japan near the boundary of the Oligocene and Miocene. The disappearance of Bering Land Bridge in the late Miocene might lead to the Eastern Asian–Eastern North American disjunction of Wisteria. Allopatric speciation of Wisteria between the Japanese archipelago and the Asian continent in the Quaternary increased the species richness of eastern Asia in comparison with eastern North America. Synonymous substitution rates (d_S) of protein-coding genes in the IRLC species were around 2-fold (SC genes) or 11-fold (IR genes) higher than those of non-IRLC species. For both SC and IR genes, herbaceous legumes have around 3-fold higher d_S than woody ones. Both loss of one IR region and herbaceous habit elevated substitution rates of the plastomes.     

Phylogeny and biogeography of Aralia sect. Aralia (Araliaceae)

Aralia sect. Aralia (Araliaceae) consists of approximately eight species disjunctly distributed in Asia and North America. Phylogenetic and biogeographic analyses were conducted using sequences of the internal transcribed spacer regions of the nuclear ribosomal DNA. Aralia racemosa from eastern North America was sister to A. californica from western North America. Aralia cordata from eastern Asia did not form a species-pair relationship with the eastern North American A. racemosa. The two subspecies of A. racemosa formed a monophyletic group. Biogeographic analyses showed a close area relationship between eastern North America and western North America. The Himalayas were cladistically basal and eastern Asia was placed between the Himalayas and North America. The biogeographic analysis supported the origin of the eastern Asian and eastern North American disjunct pattern in Aralia sect. Aralia via the Bering land bridges. Comparisons with results of phylogenetic analyses of other genera suggested that (1) the floristic connection between eastern North America and western North America may be stronger than previously thought; and (2) the biogeographic patterns in the Northern Hemisphere are complex. Furthermore, a lack of correlation between sequence divergence values and phylogenetic positions was observed, suggesting the importance of a phylogenetic framework in biogeographic analyses.     

Molecular phylogeny and phylogeography ofLupinus (Leguminosae) inferred from nucleotide sequences of therbcL gene and ITS 1 + 2 regions of rDNA

Total DNA was extracted from 55 species of theLeguminosae (including 29 species ofLupinus). The chloroplast generbcL and the ITS 1 + 2 regions of nuclear RNA genes were amplified by polymerase chain reaction (PCR) and sequenced directly. The sequences obtained were evaluated with character state (Maximum Parsimony) and distance methods (Neighbour Joining). Phylogenetic trees obtained with both data sets and methods are mostly congruent.Genisteae andCrotalarieae are sister groups and share ancestry with theThermopsideae/Podalyrieae. The genusLupinus, which forms a monophyletic clade within theGenisteae, shows a distinct Old-New World disjunction and appears to be divided into several more or less distinct groups: (1) The species from the eastern part of South America. (2) The homogeneous rough-seeded group (Scabrispermae) of the Old World species which is well distinguished from the smooth-seeded group (Malacospermae). (3) Within the rather heterogeneous smooth-seeded lupins a smaller subgroup withL. angustifolius, L. hispanicus andL. luteus is recognized. (4) Also separated are North American lupins and South American species with a western distribution. Genetic distances imply that the genusLupinus evolved during the last 12–14 million years, ruling out the hypothesis that the present Old-New World disjunction can be interpreted as a result of the continental drift. The genetic data suggest an origin in the Old World and an independant colonisation of the Eastern parts of South America as opposed to North America and the Western parts of South America.     

Phylogeny of the lizard subfamily Lygosominae (Reptilia: Scincidae), with special reference to the origin of the new world taxa

Phylogenetic relationships of the three lygosomine skink genera occurring both in the Old World and the New World (Mabuya, Scincella and Sphenomorphus) were inferred from mitochondrial DNA sequence of 12S and 16S rRNA genes. Results strongly suggested the non-monophyly for any of these three genera. Within the Mabuya group, Asian members appear to have diverged first, leaving the Neotropical and the Afro-Malagasy Mabuya as sister groups. These relationships, together with the absence of extant or fossil representatives of the Mabuya group from North America, strongly suggest the trans-Atlantic dispersals of Mabuya from Africa to Neotropics. Our results also indicated a closer affinity of the New World Scincella with the New World Sphenomorphus than with the Old World Scincella. Such relationships suggest the trans-Beringian dispersal of the common ancestor from Asia and its subsequent divergence into the North American Scincella and the Neotropical Sphenomorphus.     

Phylogenetic relationships of Loxosceles and Sicarius spiders are consistent with Western Gondwanan vicariance

The modern geographic distribution of the spider family Sicariidae is consistent with an evolutionary origin on Western Gondwana. Both sicariid genera, Loxosceles and Sicarius are diverse in Africa and South/Central America. Loxosceles are also diverse in North America and the West Indies, and have species described from Mediterranean Europe and China. We tested vicariance hypotheses using molecular phylogenetics and molecular dating analyses of 28S, COI, 16S, and NADHI sequences. We recover reciprocal monophyly of African and South American Sicarius, paraphyletic Southern African Loxosceles and monophyletic New World Loxosceles within which an Old World species group that includes L. rufescens is derived. These patterns are consistent with a sicariid common ancestor on Western Gondwana. North American Loxosceles are monophyletic, sister to Caribbean taxa, and resolved in a larger clade with South American Loxosceles. With fossil data this pattern is consistent with colonization of North America via a land bridge predating the modern Isthmus of Panama.     

紫荆属的系统发育和生物地理学研究

紫荆属（Cercis L.）约含8种,间断分布于亚洲东、西部、欧洲南部和北美。应用核糖体DNA的ITS基因序列研究紫荆属的系统发育关系。在最简约性分析,北美的两个种和南欧、西亚的一个种构成一单系群而隐藏于东亚的种类中。这表明紫荆属北美的种类和南欧、西亚的种类之间的关系比它们的各自与东亚的种类的关系要密切。研究还发现北美洲东、西部的种类可能具较近亲缘。紫荆属以白令陆桥或北大西洋陆桥为迁移途径的可能性似乎都不能排除;北半球的生物地理分布式样可具有复杂的起源。     

Molecular phylogeny and biogeography of Astilbe (Saxifragaceae) in Asia and eastern North America

Phylogenetic analyses were conducted for Astilbe (Saxifragaceae), an Asian/eastern North American disjunct genus, using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid matK, trnL‐trnF and psbA‐trnH regions. The monophyly of Astilbe is well supported by both ITS and plastid sequences. Topological incongruence was detected between the plastid and the ITS trees, particularly concerning the placement of the single North American species, A. biternata, which may be most probably explained by its origin involving hybridization and/or allopolyploidy with plastid capture. In Astilbe, all species with hermaphroditic flowers constitute a well‐supported clade; dioecious species form a basal grade to the hermaphroditic clade. Astilbe was estimated to have split with Saxifragopsis from western North America at 20.69 Ma (95% HPD: 12.14–30.22 Ma) in the early Miocene. This intercontinental disjunction between Astilbe and Saxifragopsis most likely occurred via the Bering land bridge. The major clade of Astilbe (all species of the genus excluding A. platyphylla) was inferred to have a continental Asian origin. At least three subsequent migrations or dispersals were hypothesized to explain the expansion of Astilbe into North America, Japan and tropical Asian islands. The intercontinental disjunct lineage in Astilbe invokes a hybridization event either in eastern Asia or in North America. This disjunction in Astilbe may be explained by a Beringian migration around 3.54 Ma (95% high posterior density: 1.29–6.18 Ma) in the late Tertiary, although long‐distance dispersal from eastern Asia to North America is also likely. The biogeographical connection between continental Asia, Taiwan, the Philippines and other tropical Asian islands in Astilbe provides evidence for the close floristic affinity between temperate or alpine south‐western China and tropical Asia. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Phylogeny and biogeography of Sassafras (Lauraceae) disjunct between eastern Asia and eastern North America

Sassafras (Lauraceae) consists of three species disjunct between eastern Asia (S. tzumu and S. randaiense) and eastern North America (S. albidum). Phylogenetic analysis based on sequences of nuclear ribosomal ITS and three chloroplast non-coding regions (rpl16, trnL-F, and psbA-trnH) showed that Sassafras is monophyletic and that the eastern North American S. albidum is sister to the clade of its two eastern Asian counterparts. Their intercontinental divergence was estimated to be 13.80 ± 2.29−16.69 ± 2.52 million years ago (mya) using the penalized likelihood method with the ITS and three chloroplast markers. Biogeographic analyses combined with fossil evidence suggest that Sassafras has a relict distribution in the Northern Hemisphere without a Gondwanan link. The divergence time of the two eastern Asian species (the continental Chinese Sassafras tzumu and S. randaiense endemic to Taiwan) is estimated to be 0.61 ± 0.75−2.23 ± 0.76 mya. Sassafras randaiense from Taiwan was most likely derived from an ancestor from continental China.