Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America

The genus Castanea (Fagaceae) is widely distributed in the deciduous forests of the Northern Hemisphere. The striking similarity between the floras of eastern Asia and those of eastern North America and the difference in chestnut blight resistance among species has been of interest to botanists for a century. To infer the biogeographical history of the genus, the phylogeny of Castanea was estimated using DNA sequence data from different regions of the chloroplast genome. Sequencing results support the genus Castanea as a monophyletic group with Castanea crenata as basal. The three Chinese species form a strongly supported sister clade to the North American and European clade. A unique westward expansion of extant Castanea species is hypothesized with Castanea originating in eastern Asia, an initial diversification within Asia during the Eocene followed by intercontinental dispersion and divergence between the Chinese and the European/North American species during the middle Eocene and a split between the European and the North American species in the late Eocene. The differentiation within North America and China might have occurred in early or late Miocene. The North America species are supported as a clade with C. pumila var. ozarkensis, the Ozark chinkapin, as the basal lineage, sister to the group comprising C. pumila var. pumila, the Allegheny chinkapin, and Castanea dentata, the American chestnut. Morphological evolution of one nut per bur in the genus may have occurred independently on two continents.     

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.     

Phylogenomics,biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae)

Nyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM) Nyssa talamancana was sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested that Nyssa had an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central American N. talamancana represents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals of Nyssa and the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution of Nyssa coincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution of Nyssa in EA and ENA.     

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     

Extended phylogeny of Aquilegia: the biogeographical and ecological patterns of two simultaneous but contrasting radiations

Studies of the North American columbines (Aquilegia, Ranunculaceae) have supported the view that adaptive radiations in animal-pollinated plants proceed through pollinator specialisation and floral differentiation. However, although the diversity of pollinators and floral morphology is much lower in Europe and Asia than in North America, the number of columbine species is similar in the three continents. This supports the hypothesis that habitat and pollinator specialisation have contributed differently to the radiation of columbines in different continents. To establish the basic background to test this hypothesis, we expanded the molecular phylogeny of the genus to include a representative set of species from each continent. Our results suggest that the diversity of the genus is the result of two independent events of radiation, one involving Asiatic and North American species and the other involving Asiatic and European species. The ancestors of both lineages probably occupied the mountains of south-central Siberia. North American and European columbines are monophyletic within their respective lineages. The genus originated between 6.18 and 6.57 million years (Myr) ago, with the main pulses of diversification starting around 3 Myr ago both in Europe (1.25–3.96 Myr ago) and North America (1.42–5.01 Myr ago). The type of habitat occupied shifted more often in the Euroasiatic lineage, while pollination vectors shifted more often in the Asiatic-North American lineage. Moreover, while allopatric speciation predominated in the European lineage, sympatric speciation acted in the North American one. In conclusion, the radiation of columbines in Europe and North America involved similar rates of diversification and took place simultaneously and independently. However, the ecological drivers of radiation were different: geographic isolation and shifts in habitat use were more important in Europe while reproductive isolation linked to shifts in pollinator specialisation additionally acted in North America.     

Phylogenetic relationships in Gleditsia (Leguminosae) based on ITS sequences

We used nucleotide sequences from the internal transcribed spacers and 5.8S gene of nuclear ribosomal DNA to test competing phylogenetic and biogeographic hypotheses in Gleditsia. Eleven of 13 Gleditsia species were sampled, along with two species of its sister genus, Gymnocladus. Analyses of ITS data and of a combined data set that included sequences of ITS and two chloroplast genes supported several conclusions that were interpreted in light of fossil data and current legume phylogeny. Gleditsia and Gymnocladus appear to have originated in eastern Asia during the Eocene. Eastern North American species of both genera most likely evolved from ancestors that migrated across the Bering land bridge, but the eastern Asian/eastern North American disjunction appears to be much older in Gymnocladus than in Gleditsia. Gleditsia amorphoides, from temperate South America, is sister to the rest of the genus, suggesting early long-distance dispersal from Asia. The remainder of Gleditsia is divided into three unresolved clades, possibly indicating a split early in the evolution of the genus. Two of those clades contain only Asian species, and one contains Asian and North American species. The North American species, Gleditsia triacanthos and Gleditsia aquatica, are polymorphic and paraphyletic with respect to their ITS and cpDNA sequences, which suggests recent diversification.     

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.     

Phylogeny, biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae): tracking Tertiary plant migration

Data from four DNA regions (rbcL, matK, 26S rDNA, and ITS) as well as extant and fossil morphology were used to reconstruct the phylogeny and biogeographic history of an intercontinentally disjunct plant group, the cornelian cherries of Cornus (dogwoods). The study tests previous hypotheses on the relative roles of two Tertiary land bridges, the North Atlantic land bridge (NALB) and the Bering land bridge (BLB), in plant migration across continents. Three approaches, the Bayesian, nonparametric rate smoothing (NPRS), and penalized likelihood (PL) methods, were employed to estimate the times of geographic isolations of species. Dispersal and vicariance analysis (DIVA) was performed to infer the sequence and directionality of biogeographic pathways. Results of phylogenetic analyses suggest that among the six living species, C. sessilis from western North America represents the oldest lineage, followed by C. volkensii from Africa. The four Eurasian species form a clade consisting of two sister pairs, C. mas-C. officinalis and C. chinensis-C. eydeana. Results of DIVA and data from fossils and molecular dating indicate that the cornelian cherry subgroup arose in Europe as early as the Paleocene. Fossils confirm that the group was present in North America by the late Paleocene, consistent with the DIVA predictions that, by the end of the Eocene, it had diversified into several species and expanded its distribution to North America via the NALB and to Africa via the last direct connection between Eurasia and Africa prior to the Miocene, or via long-distance dispersal. The cornelian cherries in eastern Asia appear to be derived from two independent dispersal events from Europe. These events are inferred to have occurred during the Oligocene and Miocene. This study supports the hypothesis that the NALB served as an important land bridge connecting the North American and European floras, as well as connecting American and African floras via Europe during the early Tertiary.     

New adapiform primate of Old World affinities from the Devil's Graveyard Formation of Texas

Most adapiform primates from North America are members of an endemic radiation of notharctines. North American notharctines flourished during the Early and early Middle Eocene, with only two genera persisting into the late Middle Eocene. Here we describe a new genus of adapiform primate from the Devil’s Graveyard Formation of Texas. Mescalerolemur horneri, gen. et sp. nov., is known only from the late Middle Eocene (Uintan) Purple Bench locality. Phylogenetic analyses reveal that Mescalerolemur is more closely related to Eurasian and African adapiforms than to North American notharctines. In this respect, M. horneri is similar to its sister taxon Mahgarita stevensi from the late Duchesnean of the Devil’s Graveyard Formation. The presence of both genera in the Big Bend region of Texas after notharctines had become locally extinct provides further evidence of faunal interchange between North America and East Asia during the middle Eocene. The fact that Mescalerolemur and Mahgarita are both unknown outside of Texas also supports prior hypotheses that low-latitude faunal assemblages in North America demonstrate increased endemism by the late middle Eocene.     

A NEW MICROCHOERINE OMOMYID (PRIMATES, MAMMALIA) FROM THE ENGLISH EARLY EOCENE AND ITS PALAEOBIOGEOGRAPHICAL IMPLICATIONS

Abstract:  A new genus and species of omomyid primate, Melaneremia bryanti , is described from the Early Eocene Blackheath Beds of Abbey Wood, London, UK. It shares unique derived characters with the European subfamily Microchoerinae and is its most primitive member. It is nevertheless more derived than the primitive omomyid Teilhardina belgica from the beginning of the European Eocene. Cladistic analysis shows that the Microchoerinae are sister group to a clade comprising subfamilies Omomyinae and Anaptomorphinae, but excluding Teilhardina belgica and T. asiatica , which are stem omomyids. The Mammalian Dispersal Event (MDE), which marks the beginning of the Eocene (55·8 Ma), saw the dispersal of primates, perissodactyls and artiodactyls into the Northern Hemisphere. At this time similar species of Teilhardina lived in Europe, Asia and North America. The Abbey Wood microchoerine lived about 1 million years later. It co-occurs with non-primate species identical or very similar to those that lived in North America. The latter were ground-dwellers, whereas the microchoerine and others that show distinct differences from North American relatives were tree-dwellers. Land-bridges connected North America and Europe via Greenland at the beginning of the Eocene, but 2 million years later these had been severed by submarine rifting. North American species at Abbey Wood indicate that a land connection still remained at c . 55 Ma. However, the forest belt that must have been continuous during the MDE to allow tree-dwellers to disperse between the continents is likely by this time to have been disrupted, perhaps by volcanic eruption.     

A chloroplast phylogeny of Arisaema (Araceae) illustrates Tertiary floristic links between Asia, North America, and East Africa

The evolution of Arisaema is reconstructed, based on combined sequences (2048 aligned bases) from the chloroplast trnL intron, trnL-trnF spacer, and rpl20-rps12 spacer obtained for species from all 11 sections, including sectional type species and geographically disjunct East African and North American/Mexican species. Analyses were rooted with a representative sample of the closest outgroups, Pinellia and Typhonium, to rigorously test the monophyly of Arisaema. Sections in Arisaema are mostly based on leaf, stem, and inflorescence characters and, with one exception, are not rejected by the molecular data; however, statistical support for sectional relationships in the genus remains poor. Section Tortuosa, which includes eastern North American A. dracontium and Mexican A. macrospathum, is demonstrably polyphyletic. The third New World species, A. triphyllum, also occurs in eastern North America and groups with a different Asian clade than do A. dracontium/A. macrospathum. The genus thus appears to have entered North America twice. Fossil infructescences similar to those of A. triphyllum are known from approximately 18 million-year-old deposits in Washington State and can serve to calibrate a molecular clock. Constraining the age of A. triphyllum to 18 million years (my) and applying either a semiparametric or an ultrametric clock model to the combined data yields an age of approximately 31-49 my for the divergence of A. dracontium/A. macrospathum from their Asian relatives and of 19-32 my for the divergence between African A. schimperianum and a Tibetan/Nepalese relative. The genus thus provides an example of the Oligocene/Miocene floristic links between East Africa, Arabia, the Himalayan region, China, and North America. The phylogeny also suggests secondary loss of the environmental sex determination strategy that characterizes all arisaemas except for two subspecies of A. flavum, which have consistently bisexual spathes. These subspecies are tetraploid and capable of selfing, while a third subspecies of A. flavum is diploid and retains the sex-changing strategy. In the molecular trees, the sex-changing subspecies is sister to the two non-sex-changing ones, and the entire species is not basal in the genus.     

Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes

The center of diversity is not necessarily the place of origin, as has been established by many plant molecular phylogenies. Picea is a complicated but very important genus in coniferous forests of the Northern Hemisphere, with a high species diversity in Asia. Its phylogeny and biogeography were investigated here using sequence analysis of the paternally inherited chloroplast trnC-trnD and trnT-trnF regions and the maternally inherited mitochondrial nad5 intron 1. We found that the North American P. breweriana and P. sitchensis were basal to the other spruces that were further divided into three clades in the cpDNA phylogeny, and that the New World species harbored four of five mitotypes detected, including two ancestral ones and three endemics. These results, combined with biogeographic analyses using DIVA and MacClade and fossil evidence, suggest that Picea originated in North America, and that its present distribution could stem from two times of dispersal from North America to Asia by the Beringian land bridge, and then from Asia to Europe. Most of the northeastern Asian species and the European P. abies could arise from a recent radiation given the very low interspecific genetic differentiation and pure mitotype of them. Considering that the ancestral mtDNA polymorphism can be preserved in many descendant species, even distantly related ones, we suggest that more species, at least the closely related ones, should be sampled in the phylogeographical study using cytoplasmic haplotypes if possible. In addition, we also discussed the evolution and phylogenetic utility of morphological characters in Picea.     

Evolution of East Asian ninespine sticklebacks as shown by mitochondrial DNA control region sequences

Evolutionary processes in East Asian ninespine sticklebacks (Pungitius spp.), including both extremes of armor morphology in the genus, were demonstrated with mitochondrial DNA control region (CR) phylogeny. Entire CR sequences (830-930 bp long) were determined for three species: the most heavily armored (P. sinensis), the most reduced (P. tymensis), and an intermediate (P. pungitius). The former two species are endemic to East Asia, the latter being circumpolar. Three major lineages (A, B, and C) were revealed, whereas both the phylogenetic trees and the insertion sequence dynamics supported the polyphyly of P. sinensis. Haplotypes of the mainland populations of P. sinensis possessed lineage B, being the sister group of P. tymensis lineage A. Island populations of P. sinensis, however, possessed lineage C, along with all P. pungitius haplotypes. A molecular clock hypothesis was clearly rejected for the CR sequences, significantly slower evolutionary rates being observed in the P. tymensis lineage. The split of mainland P. sinensis and P. tymensis was considered to have preceded that of the lineage C colonization in East Asia. The contrasting morphology is probably attributable to adaptation of P. tymensis to island freshwater environments and an ecological interaction between P. tymensis and lineage C emigrants.     

On the Distribution and Origin of Salix in the World

1. The distribution of Salix species among the continents. There are about 526 species of Salix in the world, most of which are distributed in the Northern Hemisphere with only a few species in the Southern Hemisphere. In Asia, there are about 375 species, making up 71.29 percent of the total in the world, including 328 endemics; in Europe, about 114 species, 21.67 percent with 73 endemics; in North America, about 91 species, 17.3 percent with 71 endemics; in Africa, about 8 species, 1.5 percent, with 6 endemics. Only one species occurs in South America. Asia, Europe and North America have 8 species in common (excluding 4 cultivated species). There are 34 common species between Asia and Europe, 14 both between Europe and North America and between Asia and North America, 2 between Asia and Africa. Acording to the Continental Drift Theory, the natural circumstances which promoted speciation and protected newly originated and old species were created by the orogenic movement of the Himalayas in the middle and late Tertiary. Besides, the air temperature was a little higher in Asia than in Europe and North America (except its west part) and the dominant glaciers were mountainous in Asia during the glacial epoch in the Quaternary Period. Then willows of Europe moved southwards to Asia. During the interglacial period they moved in opposite direction. Such a to-and-fro willow migration between Asia and Europe and between and North America occurred so often that it resulted in the diversity of willow species in Asia. Those species of willows common among the continents belong to the Arctic flora. 2. The multistaminal willows are of the primitive group in Salix. Asia has 28 species of multistaminal willows, but Europe has only one which is also found in Asia. These 28 species are divided into two groups, “northern type” and “southern type”, according to morphology of the ovary. The boundary between the two forms in distribution is at 40°N. The multistaminal willows from south Asia, Africa and South America are very similar to each other and may have mutually communicated between these continents in the Middle or Late Cretaceous Period. The southern type willows in south Asia are similar to the North American multistaminal willows but a few species. The Asian southern type willows spreaded all over the continents of Europe, Asia and North America through the communication between them before the Quaternany Period. Nevertheless, it is possible that the willows growing in North America immigranted through the middle America from South America. The Asian northern type multistaminal willows may have originated during the ice period. The multistaminal willows are more closed to populars in features of sexual organs. They are more primitive than the willows with 1-3 stamens and the most primitive ones in the genus. 3. The center of origin and development of willows Based on the above discussion it is reasonable to say that the region between 20°-40°N in East Asia is the center of the origin and differentiation of multistaminal willows. It covers Southern and Southwestern China and northern Indo-China Pennisula.     

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.     

Molecular phylogeny of osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana

One of the traditional enigmas in freshwater zoogeography has been the evolutionary origin of Scleropages formosus inhabiting Southeast Asia (the Asian arowana), which is a species threatened with extinction among the highly freshwater-adapted fishes from the order Osteoglossiformes. Dispersalists have hypothesized that it originated from the recent (the Miocene or later) transmarine dispersal of morphologically quite similar Australasian arowanas across Wallace's Line, but this hypothesis has been questioned due to their remarkable adaptation to freshwater. We determined the complete nucleotide sequences of two mitochondrial protein genes from 12 osteoglossiform species, including all members of the suborder Osteoglossoidei, with which robust molecular phylogeny was constructed and divergence times were estimated. In agreement with previous morphology-based phylogenetic studies, our molecular phylogeny suggested that the osteoglossiforms diverged from a basal position of the teleostean lineage, that heterotidines (the Nile arowana and the pirarucu) form a sister group of osteoglossines (arowanas in South America, Australasia, and Southeast Asia), and that the Asian arowana is more closely related to Australasian arowanas than to South American ones. However, molecular distances between the Asian and Australasian arowanas were much larger than expected from the fact that they are classified within the same genus. By using the molecular clock of bony fishes, tested for its good performance for rather deep divergences and calibrated using some reasonable assumptions, the divergence between the Asian and Australasian arowanas was estimated to date back to the early Cretaceous. Based on the molecular and geological evidence, we propose a new model whereby the Asian arowana vicariantly diverged from the Australasian arowanas in the eastern margin of Gondwanaland and migrated into Eurasia on the Indian subcontinent or smaller continental blocks. This study also implicates the relatively long absence of osteoglossiform fossil records from the Mesozoic.     

Phylogenetic relationships among New World Scrophularia L. (Scrophulariaceae): new insights inferred from DNA sequence data

The genus Scrophularia L. (Scrophulariaceae) comprises 200?C300 species, of which approximately 19 are distributed in North America and the Greater Antilles. To investigate phylogenetic and biogeographic relationships of the New World species, two intergenic spacers (trnQ-rps16 and psbA-trnH) of chloroplast DNA and nuclear ribosomal ITS were sequenced. Phylogenetic analyses revealed three distinct New World clades that correspond to their geographical distribution and are corroborated by morphological characters. Phylogenetic inference indicates the eastern American S. marilandica L. as sister to all Antillean species; for colonization of the Caribbean archipelago, a late Miocene dispersal event from the North American mainland is assumed. There is evidence for a hybrid origin of the most widespread North American species, S. lanceolata Pursh. The results further suggest that S. nodosa L. is sister to all New World and three Japanese species of Scrophularia. The latter form an Eastern Asian?CEastern North American (EA-ENA) disjunction with six New World species. We propose an eastern Asian origin for the New World taxa of Scrophularia. Divergence times estimated using a relaxed molecular clock model suggest one or more Miocene migration events from eastern Asia to the New World via the Bering Land Bridge followed by diversification in North America.     

Discordance between phylogenetics and coalescent-based divergence modelling: exploring phylogeographic patterns of speciation in the Carex macrocephala species complex

We fit a molecular data set, consisting of the rpL16 cpDNA marker and eight microsatellite loci, to the isolation-with-migration model as implemented in IM a to test a well-supported phylogenetic hypothesis of relationships within the Carex macrocephala species complex (Cyperaceae). The phylogenetic hypothesis suggests C. macrocephala from North America is reciprocally monophyletic and is sister to a reciprocally monophyletic clade of C. kobomugi . The North American C. macrocephala and C. kobomugi clade form a sister clade with a lineage of Asian C. macrocephala , thereby forming a paraphyletic C. macrocephala species. Not only does the phylogenetic hypothesis suggest C. macrocephala is paraphyletic, but it also suggests that the two lineages which share a partially overlapping distribution, Asian C. macrocephala and C. kobomugi , are not the most closely related. To test these relationships, we used coalescent-based population genetic models to infer divergence time for each lineage pair within the species complex. The coalescent-based models account for the stochastic forces which drive population divergence, and can account for the lineage sorting that occurs prior to lineage divergence. A drawback to phylogenetic-based phylogeographical analyses is that they do not account for stochastic lineage sorting that occurs between gene divergence and lineage divergence. By comparing the relative divergence time of the three main lineages within this group, Asian C. macrocephala , North American C. macrocephala , and C. kobomugi , we concluded that the phylogenetic hypothesis is incorrect, and the divergence between these lineages occurred during the Late Pleistocene epoch.