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.     

Molecular phylogenetics of tribe Synandreae, a North American lineage of lamioid mints (Lamiaceae)

The five mint genera Brazoria, Macbridea, Physostegia, Synandra and Warnockia (Lamioideae: Lamiaceae) are all North American endemics. Together with the monotypic European genus Melittis and the Asian genus Chelonopsis, these taxa have been classified as subtribe Melittidinae. Previous morphological studies have failed to uncover synapomorphic characters for this group. We sequenced the plastid trnL‐trnF region and trnS‐trnG spacer and the nuclear ribosomal 5S non‐transcribed spacer (5S‐NTS) to assess phylogenetic relationships within Melittidinae. Standard parsimony and direct optimization (POY) analyses show Melittis, the type genus of the subtribe, as sister to Stachys. Thus, the monophyly of subtribe Melittidinae is not supported either by molecular or morphological data. However, the North American endemics form a monophyletic group that can be recognized as the recircumscribed tribe Synandreae. The molecular relationships among these genera are corroborated by both morphological and cytological data. The expected close relationship between the south‐central endemics Warnockia and Brazoria and their sister relationship to the widespread genus Physostegia is confirmed. Nevertheless, most of the North American endemics are restricted to the south‐east of the continent. Dispersal westwards and northwards is correlated with an increase in chromosome numbers. No specific Eurasian origin (i.e., transatlantic or transpacific) can be determined, but Synandreae are clearly distinct from the large Stachys clade, and therefore represent a separate migration into North America. © The Willi Hennig Society 2007.     

Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus,Nothofagaceae)

Subgenus Nothofagus, although geographically restricted at present to temperate areas of South America, has captured much attention in discussions of plant biogeography due to its widespread distribution through Gondwanan continents during the Tertiary. However, phylogenetic relationships within the subgenus Nothofagus have not yet been resolved. We examined geographic patterns of intraspecific and interspecific genetic variation to detect whether incongruences in nuclear or plastid DNA phylogenies occur, in order to better understand the evolutionary history of the subgenus Nothofagus. We conducted spatially-explicit sampling at 10 distinct locations throughout the range of austral South American forests and sampled all present Nothofagus species. We used ITS and chloroplast DNA sequences to estimate phylogenetic relationships. A phylogeny constructed from nuclear genes resolved the subgenus Nothofagus as monophyletic. We found that N. antarctica was a sister to a clade of evergreen species (N. betuloides, N. dombeyi, and N. nitida), while N. pumilio likely diverged earlier. Nine cpDNA haplotypes were distinguished in the subgenus Nothofagus which were associated to geographic locations rather than to taxonomic relationships. This species-independent cpDNA phylogeographic structures within the subgenus Nothofagus may be related to repeated chloroplast capture events over geological time in Patagonia.     

Towards a phylogeny of Cyclops (Copepoda): (in)congruences among morphology,molecules and zoogeography

The phylogeny of Cyclops (~30 spp.), a predominantly Palearctic cold‐adapted genus, was reconstructed based on morphological and molecular characters. The morphological analysis used extensive taxon sampling from the entire Holarctic range of the genus and included 53 morphological characters. Polymorphic traits were coded by the “unordered,” “unscaled” and “scaled” methods; maximum parsimony criterion was applied in tree building. Molecular phylogenetic reconstructions utilized partial nuclear 18S and 28S ribosomal genes, mitochondrial cytochrome oxidase I and complete internal transcribed spacer regions I and II, albeit with limited taxon sampling. Bayesian inference and maximum likelihood were used in these tree reconstructions. The molecular characters were used both in combination with morphology and as an independent test of the basal relationships inferred from morphology. Monophyly of the genus received strong support in both the morphological and molecular phylogenies; the basal relationships remain unresolved. The morphology‐based phylogenies, along with the geographic distribution patterns and ecological traits, supported monophyly of the ankyrae?ladakanus clade, scutifer‐clade (C. scutifer, C. jashnovi, C. columbianus), kolensis‐clade (C. kolensis, C. kikuchii, C. vicinus, C. furcifer, C. insignis, C. alaskaensis), abyssorum‐clade (C. abyssorum s. str., C. abyssorum larianus, C. ricae, C. sevani) and divergens‐clade (South Carpathian “Cyclops sp. Y,” C. mauritaniae, C. divergens, C. bohater, C. lacustris). Relationships among European and North American populations of C. scutifer and C. columbianus based on partial sequences of the 12S mitochondrial gene show C. scutifer to be paraphyletic, suggesting two independent invasions into North America via the Bering Land Bridge from Siberia to Alaska.     

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.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.     

Phylogenetics of the marine sculpins (Teleostei: Cottidae) of the North American Pacific Coast

With 92 species along the North American Pacific Coast, marine sculpins represent the most species-rich radiation of fishes in this region. I used the mitochondrial cytochrome b gene and the nuclear ribosomal S7 intron for 99 species (76 North American, 19 Asian, and four North Atlantic) to produce the most complete phylogenetic hypothesis yet generated for this assemblage. Maximum likelihood and Bayesian analyses produced highly similar tree topologies. While many previously proposed groupings based on morphology are recovered, the molecular data suggest that a number of genera are para- or polyphyletic. However, this analysis supports the monophyly of one large clade that is found exclusively along the North American Pacific Coast (Chitonotous–Ruscarius–Artedius–Orthonopius–Clinocottus–Leiocottus–Oligocottus). Some sibling species have disjunct ranges, suggesting allopatric speciation. However, many other sibling species have largely overlapping ranges, and repeated habitat shifts appear to have facilitated diversification.     

Desmophyllum dianthus (Esper, 1794) in the Scleractinian Phylogeny and Its Intraspecific Diversity

The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the “robust” clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.     

Comparative phylogeography of Amphicarpaea legumes and their root-nodule symbionts in Japan and North America

Aim Relationships of eastern Asian and eastern North American populations of legumes in the genus Amphicarpaea Elliot ex. Nuttall (Phaseoleae–Glycininae) and their root nodule bacteria (Bradyrhizobium Jordan) were analysed to test whether both organisms share an identical biogeographic history. Location Japan and eastern North America (New York and Illinois). Methods Sequences of three plant genes (chloroplast trnL region, nuclear ribosomal ITS, and histone H3‐D) and a segment of the bacterial ribosomal region (partial 16S rRNA and 23S rRNA genes, and the 16S rRNA–23S rRNA ITS) were used to analyse phylogenetic relationships. Results For plants, Japanese populations formed a sister group to a well‐supported clade of all North American genotypes. For nodule bacteria associated with Amphicarpaea, isolates from North America did not form a single clade relative to Asian genotypes. Japanese Bradyrhizobium isolates were closely related to particular sub‐groups of North American bacteria (lineages ‘B’ and ‘C’), with other American bacteria branching earlier. Main conclusions Plants and bacteria showed clear deviations from a pattern of parallel cladogenesis. The most basal Amphicarpaea lineage was associated with a recently‐diverged bacterial group, while one recently‐diverged plant lineage had symbionts that branched in a basal position relative to the other Amphicarpaea bacteria. When analysed with data on symbiotic compatibility from inoculation experiments, the molecular phylogenies suggested that for plants, at least one transition has occurred toward more promiscuous nodulation behaviour. Among bacteria, strains with narrow host range on Amphicarpaea appear to be ancestral to symbiotic generalists.     

Phylogenetic estimation of Mytilidae in the East China Sea inferred from mitochondrial genes and nuclear DNA sequence variation

We performed a phylogenetic estimation of the family Mytilidae in the East China Sea based on nuclear internal transcribed spacer (ITS) genes and two mitochondrial genes (COI and 16S RNA). Analysis of five mytilid species based on each of the three genes resulted in mostly congruent trees, although there were some discrepancies in the classification of these species. We combine the results obtained from the three separate analyses to provide a phylogenetic estimation of Mytilidae. We found that the Mytilidae was divided into two major lineages: in one clade, Mytilus galloprovincialis was grouped with Mytilus coruscus; in the second clade, Septifer bilocularis was placed at the basal position in an individual clade, and Perna viridis and Musculista senhousia were recovered as a monophyletic group. Although these finding provide important insights into the taxonomic relationships among the Mytilidae, many aspects of Mytilidae phylogeny remain unresolved. Further analysis based on more molecular information and extensive taxon sampling is necessary to elucidate the phylogenetic relationships among the major lineages within the Mytilidae.     

Phylogenetic relationships of the rare Korean monotypic endemic genus Pentactina Nakai in the tribe Spiraeeae (Rosaceae) based on molecular data

The phylogenetic position of Pentactina Nakai, one of only six endemic genera in the Korean peninsula, has been elusive and difficult to determine due to inaccessibility of plant materials. In this paper, we were able to obtain material from the one and only living collection of Pentactina outside of its native range in North Korea and determined its phylogenetic relationship relative to the other genera within the tribe Spiraeeae (Rosaceae). This paper presents the first molecular phylogeny of the genus Pentactina using both nuclear ribosomal ITS regions as well as chloroplast DNA trnL-trnF intergenic spacers to conduct phylogenetic analyses (maximum parsimony and maximum likelihood) of the Spiraeeae. The ITS and combined data set trees suggest that Pentactina shares its most recent common ancestor with Petrophyton, a small western North American genus, while cpDNA suggests close relationships to Kelseya, Sibiraea, and Petrophyton. Therefore, based on the present molecular sequence data, we suggest that the rare Korean monotypic endemic genus Pentactina possibly has a close relationship with the small western North American genus Petrophyton, although receiving a weak support. In addition, our current study suggests that Pentactina is not part of the large genus Spiraea as previously hypothesized by Hutchinson. Pentactina possess combinations of several morphological features within the Spiraeeae such as an erect shrub habit, simple serrate leaves, and raceme inflorescences, and recognition as a distinct endemic genus in Korea is warranted.     

Mitochondrial <Emphasis Type="Italic">matR</Emphasis> sequences help to resolve deep phylogenetic relationships in rosids

Background  

Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrial matR gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of matR in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including matR, two plastid genes (rbcL, atpB), and one nuclear gene (18S rDNA).     

Phylogeny of Cleome L. and its close relatives Podandrogyne Ducke and Polanisia Raf. (Cleomoideae, Cleomaceae) based on analysis of nuclear ITS sequences and morphology

A phylogenetic survey of representatives from all New World and several Old World supraspecific groupings of Cleome, as well as from the closely related Podandrogyne and Polanisia, was conducted based on separate analysis of nuclear ribosomal ITS sequences and of morphological characters. Parsimony analysis of the molecular data recognized this group of cleomoid taxa as a strongly supported monophyletic lineage. Podandrogyne was imbedded within a highly supported Andinocleome clade, whereas Polanisia was placed as a member of a North American/Old World Cleome s. l. clade but with low support. The ITS data also indicated the sequential divergence of several basal Old World (sects. Cleome, Gymnogonia, Ranmanissa and Rutidosperma) and North American (subg. Physospermon, sect. Peritoma) lineages followed by more recent splittings of Central and South American lineages (the Andinocleome (sects. Pterosperma and Rimosperma) group, and sects. Melidiscus and Tarenaya). The morphological data showed extensive homoplasy and did not resolve the phylogeny of these cleomoids, although the cladistic analysis distinguished two poorly supported (subg. Eucleome and sect. Tarenaya) clades. Despite this, several sets of morphological and chromosomal secondary synapomorphies served to characterize the main sectional clades recovered in the molecular tree. Based on the strong support of the Cleome + Podandrogyne + Polanisia clade and the insufficient resolution and low support of the basal branches of this tree, and on the inherent homoplasy and unsatisfactory resolution of the morphological diagnostic traits used to characterize these taxa, a reunification of the three cleomoid genera under a large genus Cleome s. l. would be advisable. A biogeographical interpretation of our molecular phylogeny indicated and earlier origin of the ancestral Cleome lineages in the Old World, followed by colonization of North America and then a subsequent expansion towards central and South American with more recent secondary radiations in these subcontinents.     

Chasing ghosts: the phylogeny of Amaurobioidinae ghost spiders (Araneae,Anyphaenidae)

The family Anyphaenidae, also known as ghost spiders, includes a diverse array of nocturnal cursorial spiders that actively hunt on vegetation. The family is mostly distributed in the Americas and has been traditionally divided into three subfamilies. The mostly tropical and North American Anyphaeninae and the Amaurobioidinae, primarily distributed in southern South America, hold the bulk of the diversity, while the Malenellininae includes a single Chilean species. Here, we use a combined morphological and molecular approach to infer the relationships of the subfamily Amaurobioidinae and examine the delimitation of contentious genera. The morphological characters include both genitalic and somatic morphology, whereas molecular data include four markers, two mitochondrial (COI, 16S) and two nuclear (28S, H3). All our analyses agree on the monophyly of Amaurobioidinae, Amaurobioidini, Gayennini, the genera Negayan, Amaurobioides, Josa, Araiya, Arachosia and Monapia, as well as the paraphyly of Anyphaeninae. The total evidence analysis supports the novel placement of Josa as the sister group of both tribes Amaurobioidini and Gayennini, most of the previously known intergeneric relationships within Gayennini, and a clade of Amaurobioidini with a projecting ocular area, including Aysenoides, Axyracrus, Amaurobioides and Aysenia. The sequence data solve the puzzling placement of Philisca puconensis, here transferred to Tomopisthes, and Tasata chiloensis, transferred to Oxysoma. The advantages of the total evidence phylogenetic approach and the evolution of the male copulatory organ are discussed.     

Phylogeny,biogeography and ecological diversification of Sarcocornia (Salicornioideae,Amaranthaceae)

Background and Aims Sarcocornia comprises about 28 species of perennial succulent halophytes distributed worldwide, mainly in saline environments of warm-temperate and subtropical regions. The genus is characterized by strongly reduced leaves and flowers, which cause taxonomic difficulties; however, species in the genus show high diversity in growth form, with a mat-forming habit found in coastal salt marshes of all continents. Sarcocornia forms a monophyletic lineage with Salicornia whose species are all annual, yet the relationship between the two genera is poorly understood. This study is aimed at clarifying the phylogenetic relationship between Sarcocornia and Salicornia, interpreting biogeographical and ecological patterns in Sarcocornia, and gaining insights into putative parallel evolution of habit as an adaptation to environmental factors.Methods A comprehensively sampled and dated phylogeny of Sarcocornia is presented based on nuclear ribosomal DNA (external transcribed spacer) and chloroplast DNA (atpB-rbcL, rpl32-trnL) sequences; representative samples of Salicornia were also included in the analyses. To infer biogeographical patterns, an ancestral area reconstruction was conducted.Key Results The Sarcocornia/Salicornia lineage arose during the Mid-Miocene from Eurasian ancestors and diversified into four subclades: the Salicornia clade, the American Sarcocornia clade, the Eurasian Sarcocornia clade and the South African/Australian Sarcocornia clade. Sarcocornia is supported as paraphyletic, with Salicornia nested within Sarcocornia being sister to the American/Eurasian Sarcocornia clade. The American and the South African/Australian Sarcocornia clade as well as the Salicornia clade were reconstructed to be of Eurasian origin. The prostrate, mat-forming habit arose multiple times in Sarcocornia.Conclusions Sarcocornia diversified in salt-laden environments worldwide, repeatedly evolving superficially similar prostrate, mat-forming habits that seem advantageous in stressed environments with prolonged flooding, high tidal movement and frost. Some of these prostrate-habit types might be considered as ecotypes (e.g. S. pacifica or S. pillansii) while others represent good ecospecies (e.g. S. perennis, S. decumbens, S. capensis), hence representing different stages of speciation.     

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.     

Phylogenetic relationships and biogeographic patterns in North American members of Carex section Acrocystis (Cyperaceae) using nrDNA ITS and ETS sequence data

Carex section Acrocystis currently includes 27 taxa in North America. Recent phylogenetic studies have suggested that the North American and some but not all of the Eurasian species form a clade. Relationships and biogeographic patterns among species in this core-Acrocystis group are explored here using nuclear ribosomal (nrDNA) internal transcribed spacer region (ITS) and nrDNA external transcribed spacer region (ETS) sequence data. While maximum parsimony analysis of the ITS and ETS data provides only a moderately resolved branching structure for species relationships within the core-Acrocystis clade, maximum likelihood analysis provides a more resolved hypothesis of relationships in the section. The core-Acrocystis clade consists of a grade of Eurasian and primarily western North American species, with a well-supported clade of only eastern North American species nested within this grade. ITS and ETS types do not coalesce within many species or species complexes. Possible explanations for the non-coalescent nature of ITS and ETS copies in Acrocystis are explored, including lineage sorting, hybridization, and cryptic species.     

Phylogeography of the fungal pathogen Histoplasma capsulatum

Until recently, Histoplasma capsulatum was believed to harbour three varieties, var. capsulatum (chiefly a New World human pathogen), var. duboisii (an African human pathogen) and var. farciminosum (an Old World horse pathogen), which varied in clinical manifestations and geographical distribution. We analysed the phylogenetic relationships of 137 individuals representing the three varieties from six continents using DNA sequence variation in four independent protein‐coding genes. At least eight clades were idengified: (i) North American class 1 clade; (ii) North American class 2 clade; (iii) Latin American group A clade; (iv) Latin American group B clade; (v) Australian clade; (vi) Netherlands (Indonesian?) clade; (vii) Eurasian clade and (viii) African clade. Seven of eight clades represented genetically isolated groups that may be recognized as phylogenetic species. The sole exception was the Eurasian clade which originated from within the Latin American group A clade. The phylogenetic relationships among the clades made a star phylogeny. Histoplasma capsulatum var. capsulatum individuals were found in all eight clades. The African clade included all of the H. capsulatum var. duboisii individuals as well as individuals of the other two varieties. The 13 individuals of var. farciminosum were distributed among three phylogenetic species. These findings suggest that the three varieties of Histoplasma are phylogenetically meaningless. Instead we have to recognize the existence of genetically distinct geographical populations or phylogenetic species. Combining DNA substitution rates of protein‐coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America.     

Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data

Previous phylogenetic analyses of Ranunculales, which have mostly been focused on an individual family and were based on molecular data alone, have recovered three main clades within the order. However, support for relationships among these three clades was weak. Earlier hypotheses were often hampered by limited taxon sampling; to date less than one-tenth of the genera in the order have been sampled. In this study, we used a greatly enlarged taxon sampling (105 species, representing 99 genera of all seven families in the order). Our study is, furthermore, the first to employ morphology (65 characters) in combination with sequence data from four genomic regions, including plastid rbcL, matK and trnL-F, and nuclear ribosomal 26S rDNA to reconstruct phylogenetic relationships within Ranunculales. Maximum parsimony and Bayesian inference were performed on the individual and combined data sets. Our analyses concur with those of previous studies, but in most cases provide stronger support and better resolution for relationships among the three main clades retrieved. The first, comprised solely of the monogeneric family Eupteleaceae, is the earliest-diverging lineage. The second clade is composed exclusively of taxa of Papaveraceae, which is sister to the third clade, the core Ranunculales, comprising the other five families of the order. Circaeasteraceae and Lardizabalaceae form a strongly supported clade. Pteridophyllum is supported as sister to Hypecoum, contradicting the viewpoint that the former is the earliest-diverging genus in Papaveraceae. Glaucidium is basalmost in Ranunculaceae. Within this phylogenetic framework, the evolution of selected characters is inferred and diagnostic morphological characters at different taxonomic levels are identified and discussed. Based on both morphological and molecular evidence, a classification outline for Ranunculales is presented, including the proposal of two new subfamilies, Menispermoideae and Tinosporoideae in Menispermaceae and a new tribe, Callianthemeae, for the genus Callianthemum (Ranunculaceae).     

Phylogenetic Relationships of Pogoniinae (Vanilloideae, Orchidaceae): An Herbaceous Example of the Eastern North America-Eastern Asia Phytogeographic Disjunction

rb cL DNA sequences, nuclear ribosomal ITS DNA sequences, morphology, and combined evidence. All these matrices produced patterns that agree on the broader Phylogenetic relationship within the clade. Duckeella is sister to all Pogoniinae, South American species of Cleistes are monophyletic, Pogonia is monophyletic and part of a larger clade of temperate taxa (Isotria, Pogonia, and Cleistes divaricata) from North America and Asia. The structure of the cladograms and the high levels of bootstrap support strongly indicate that the genus Cleistes is paraphyletic. The disjunction between tropical South American and temperate North American taxa as well as the disjunction between Pogonia ophioglossoides in eastern North America with P. minor and P. Japonica in eastern Asia are best explained by speciation following a northward longdistance dispersal and subsequent northwestward migration via Bering land bridges in the Tertiary. This phylogenetic study adds an additional herbaceous example to the growing list of plants that demonstrate this classical biogeographic pattern. Received 5 February 1999/ Accepted in revised form 9 June 1999