Phylogeny of ips DeGeer species (Coleoptera: scolytidae) inferred from mitochondrial cytochrome oxidase I DNA sequence

We used 766 bp of DNA sequence data from the mitochondrial cytochrome oxidase I gene to reconstruct a phylogeny for 39 of 43 Ips species, many of which are economically important bark beetles. The phylogeny was reconstructed using equally weighted and weighted parsimony. In both analyses, peripheral clades were well supported while internal clades were poorly supported. Phylogenetic analysis of translated amino acids produced a poorly resolved tree that was discordant with trees reconstructed with nucleotide sequence data. Two main conclusions are drawn about the monophyly of Ips and traditional systematic groups within Ips. First, Ips is monophyletic only when I. mannsfeldi, I. nobilis, and the concinnus and latidens species groups are excluded. The latidens group, I. mannsfeldi, and I. nobilis form a monophyletic group with 3 Orthotomicus species, while the concinnus group has a more basal position. Second, the majority of the species groups in the current classification for Ips are not monophyletic. European Ips species do not form a monophyletic group, contrary to common usage, and are dispersed on the phylogenetic tree among North American species. These results indicate that a formal systematic revision of Ips is needed.     

Role of ipsdienol, ipsenol, and cis-verbenol in chemical ecology of Ips avulsus, Ips calligraphus, and Ips grandicollis (Coleoptera: Curculionidae: Scolytinae)

Stressed or damaged pine (Pinus sp.) trees in the southeastern United States are often colonized simultaneously by three southern Ips species (Coleoptera: Curculionidae: Scolytinae): small southern pine engraver, Ips avulsus (Eichhoff); sixspined ips, Ips calligraphus (Germar); and eastern fivespined ips, Ips grandicollis (Eichhoff). All three species mediate colonization of host material with volatile pheromones. All of the southern Ips produce cis-verbenol, and either ipsdienol or ipsenol, and electrophysiological studies have demonstrated that all three southern Ips are able to detect all three compounds. This study examined the role of ipsdienol, ipsenol, and cis-verbenol in the chemical ecology of the southern Ips in Georgia and Louisiana. The most attractive blends of pheromones, with the fewest number of components, were ipsdienol plus ipsenol for I. avulsus, cis-verbenol plus ipsdienol for I. calligraphus, and either cis-verbenol plus ipsenol or ipsdienol plus ipsenol for I. grandicollis. Cross-attraction of I. grandicollis to the pheromone blend most attractive to I. avulsus was observed. Although the presence of heterospecific pheromone reduced the catches of all three species (i.e., the tertiary blend captured fewer beetles than the most attractive binary blends) in both states (significantly in two cases), high numbers of all three species were still captured in traps baited with all three compounds. These results suggest that the pheromones cis-verbenol, ipsdienol, and ipsenol can be combined for monitoring all three species of the southern Ips simultaneously.     

Genetic and Morphological Differentiation of the Indo-West Pacific Intertidal Barnacle Chthamalus malayensis

Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of sequences of mitochondrial cytochrome c oxidase subunit I reveals four genetically differentiated clades with almost allopatric distribution in this region. The four clades exhibit morphological differences in arthropodal characters, including the number of conical spines and number of setules of the basal guard setae on the cirri. These characters are, however, highly variable within each clade; such that the absolute range of the number of conical spines and setules overlaps between clades, and therefore, these are not diagnostic characters for taxonomic identification. The geographic distribution of the four clades displays a strong relationship between surface temperatures of the sea and ocean-current realms. The Indo-Malay (IM) clade is widespread in the tropical, equatorial region, including the Indian Ocean, Malay Peninsula, and North Borneo. The South China (SC) and Taiwan (TW) clades are found in tropical to subtropical regions, with the former distributed along the coasts of southern China, Vietnam, Thailand, and the western Philippines under the influence of the South China Warm Current. The TW clade is endemic to Taiwan, while the Christmas Island (CI) clade is confined to CI. There was weak or no population subdivision observed within these clades, suggesting high gene flow within the range of the clades. The clades demonstrate clear signatures of recent demographic expansion that predated the Last Glacial Maximum (LGM), but they have maintained a relatively stable effective population in the past 100,000 years. The persistence of intertidal fauna through the LGM may, therefore, be a common biogeographic pattern. The lack of genetic subdivision in the IM clade across the Indian and Pacific Oceans may be attributed to recent expansion of ranges and the fact that a mutation-drift equilibrium has not been reached, or the relaxed habitat requirements of C. malayensis that facilitates high concurrent gene flow. Further studies are needed to determine between these alternative hypotheses.     

Species identification of Hypoderma affecting domestic and wild ruminants by morphological and molecular characterization

Cuticular structures and the sequence of the cytochrome oxidase I gene were compared for Hypoderma bovis (Linnaeus), Hypoderma lineatum (De Villers), Hypoderma actaeon Brauer, Hypoderma diana Brauer and Hypoderma tarandi (Linnaeus) (Diptera, Oestridae). Third-stage larvae of each species were examined by scanning electron microscopy revealing differences among species in the pattern and morphology of spines on the cephalic and thoracic segments, by spine patterns on the tenth abdominal segment, and by morphology of the spiracular plates. The morphological approach was supported by the molecular characterization of the most variable region of the cytochrome oxidase I (COI) gene of these species, which was amplified by polymerase chain reaction and analysed. Amplicons were digested with the unique restriction enzyme, BfaI, providing diagnostic profiles able to simultaneously differentiate all Hypoderma species examined. These findings confirm the utility of morphological characters for differentiating the most common Hypoderma larvae and reconfirm the power of the COI gene for studying insect identification and systematics.     

Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae,Conflicting with Current Classification Schemes

Urticaceae is a family with more than 2000 species, which contains remarkable morphological diversity. It has undergone many taxonomic reorganizations, and is currently the subject of further systematic studies. To gain more resolution in systematic studies and to better understand the general patterns of character evolution in Urticaceae, based on our previous phylogeny including 169 accessions comprising 122 species across 47 Urticaceae genera, we examined 19 diagnostic characters, and analysed these employing both maximum-parsimony and maximum-likelihood approaches. Our results revealed that 16 characters exhibited multiple state changes within the family, with ten exhibiting >eight changes and three exhibiting between 28 and 40. Morphological synapomorphies were identified for many clades, but the diagnostic value of these was often limited due to reversals within the clade and/or homoplasies elsewhere. Recognition of the four clades comprising the family at subfamily level can be supported by a small number carefully chosen defining traits for each. Several non-monophyletic genera appear to be defined only by characters that are plesiomorphic within their clades, and more detailed work would be valuable to find defining traits for monophyletic clades within these. Some character evolution may be attributed to adaptive evolution in Urticaceae due to shifts in habitat or vegetation type. This study demonstrated the value of using phylogeny to trace character evolution, and determine the relative importance of morphological traits for classification.     

Molecular systematics of the Awaous banana complex (River gobies; Teleostei: Oxudercidae)

Diadromous fishes can exhibit interesting evolutionary and population-level patterns given their use of freshwater and marine environments as part of their life histories. The River goby genus Awaous are prominent members of riverine ichthyofaunas and occur throughout Atlantic and Pacific slopes of the Americas from the southern United States to Ecuador and Brazil. Here we study the widespread and polymorphic Awaous banana complex to assess phylogeographic patterns and test previous hypotheses that all populations of this species in the Americas belong to the same species. Analysis of sequence data based on the mitochondrial cytochrome oxidase I gene shows multiple clades within the Atlantic and Pacific basins, which correspond to previously described species. Additionally, haplotype analysis demonstrates unique and unconnected networks between these species. Within these clades we document biogeographic patterns that are congruent with results of other co-occurring diadromous species, as well as a novel biogeographic pattern for the region. Our results support the recognition of distinct species of Awaous in the Atlantic (A. banana and A. tajasica) and Pacific (A. transandeanus) basins. These results are concordant with previously established morphological characters permitting the separation of these species.     

Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning

The phylogenetic relationships among the southern African freshwater crab species were examined using partial sequence data from three mitochondrial genes (12S rRNA, 16S rRNA, and mtDNA COI) 26 morphological characters and 14 allozyme loci. The aims of the present study were firstly to determine whether freshwater crab species that live in the same geographic region share a close phylogenetic relationship. Secondly, to investigate whether hybridizing species are genetically closely related and thirdly, to test for the validity of subgenera based on the genetic data sets. Phylogenetic analysis based on sequence data revealed largely congruent tree topologies and some associations had consistently high bootstrap support, and these data did not support Bott's subgeneric divisions. The morphological data were less informative for phylogenetic reconstruction while the allozyme data generally supported patterns recovered by the sequence data. A combined analysis of all the data recovered two monophyletic clades, one comprised of small-bodied mountain stream species and the other clade consisting of large-bodied riverine species. The combined analyses reflected clear biogeographic patterning for these river crabs. In addition, there was a clear correlation between genetic distance values and the ability of sympatric species to hybridize.     

A molecular phylogeny of Anopheles annulipes (Diptera: Culicidae) sensu lato: the most species-rich anopheline complex

The Australasian Annulipes Complex is the most species-rich among Anopheles mosquitoes, with at least 15 sibling species suspected. Members of this complex are the most likely vectors of malaria in the past in southern Australia and are involved in the spread of myxomatosis among rabbits. In this, the first comprehensive molecular study of the Annulipes Complex, 23 ITS2 rDNA variants were detected from collections throughout Australia and Papua New Guinea, including diagnostic variants for the previously identified An. annulipes species A-G. Specimens of each ITS2 variant were sequenced for portions of the mitochondrial COI, COII and nuclear EF-1alpha genes. Partitioned Bayesian and Maximum Parsimony analyses confirmed the monophyly of the Annulipes Complex and revealed at least 17 clades that we designate species A-Q. These species belong to two major clades, one in the north and one mainly in the south, suggesting that climate was a driver of species radiation. We found that 65% (11) of the 17 sibling species recorded here had unique COI sequences, suggesting that DNA barcoding will be useful for diagnosing species within the Annulipes Complex. A comparison of the taxa revealed morphological characters that may be diagnostic for some species. Our results substantially increase the size of the subgenus Cellia in Australasia, and will assist species-level studies of the Annulipes Complex.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Revision of the fishfly genus Ctenochauliodes van der Weele (Megaloptera, Corydalidae)

The first taxonomic revision and phylogenetic analysis of the Oriental fishfly genus Ctenochauliodes van der Weele, 1909 is presented. Except for C. punctulatus , where the male is unknown, all species of Ctenochauliodes and two outgroups ( Archichauliodes chilensis Kimmins and Protochauliodes bullocki Flint) were scored for 24 adult morphological characters, 21 of which were obtained from the male genitalia. The monophyly of Ctenochauliodes is corroborated by a series of synapomorphic characters. The pectinate female antenna was proposed as a diagnostic character. Two main clades within Ctenochauliodes were found based on the present phylogenetic analysis. All 12 Ctenochauliodes species are keyed, described and illustrated, with five species new to science. Ctenochauliodes forcipatus Kimmins is a junior synonym of C. friedrichi Navás, and C. moganshanus Yang & Yang is a junior synonym of C. griseus Yang & Yang. All Ctenochauliodes species were recorded from southern China, including 11 endemic species. Hence, there is no doubt that southern China should be acknowledged as the distribution centre of Ctenochauliodes .     

Phylogeny and biogeography of a large radiation of Andean lizards (Iguania, Stenocercus)

With 61 species occurring mostly in the Andes and adjacent lowland areas, Stenocercus lizards represent one of the most widespread and well-represented Andean vertebrate groups. Phylogenetic relationships among species of Stenocercus are inferred using different datasets based on mitochondrial DNA sequence data of 35 species and morphological data of 59 species. Among morphological data, polymorphic and meristic/morphometric characters are coded under the frequency parsimony and gap-weighting methods, respectively, and the accuracy of these methods is tested. When both types of characters are included, the resulting tree topology is more similar to the topologies obtained from analyses of DNA sequence data than those topologies obtained after exclusion of one or both types of characters. The phylogenetic hypotheses inferred including 59 species of Stenocercus (dataset 1) and excluding those species for which DNA data were not available (dataset 2) are generally congruent with each other, as well as with previously published hypotheses. The most parsimonious tree obtained from analysis of dataset 2 is used in a dispersal-vicariance analysis to infer ancestral areas and major biogeographical events. Species of Stenocercus are divided into two major clades. Clade A has diversified mostly in the central Andes, with a few species in the northern Andes and one species in the southern Andes. Clade B is more widespread, with species in the northern, central, and southern Andes, as well as in the Atlantic lowlands and Amazon basin. The most recent common ancestor of Stenocercus is inferred to have occurred in the eastern cordillera of the central Andes. Given morphological similarity and altitudinal distribution of some species nested in a northern-Andes clade, as well as the relatively recent uplift of this Andean region, it is possible that species in this clade have diverged as recently as the mid-Pliocene.     

Morphological and mitochondrial DNA divergence validates blackmouth, Galeus melastomus, and Atlantic sawtail catsharks, Galeus atlanticus, as separate species

A total of 60 morphometric traits and nucleotide sequences of the entire mtDNA NADH dehydrogenase subunit 2 (ND2) gene [1047 base pair (bp)] in 23 individuals of blackmouth, Galeus melastomus , and 13 individuals of sawtail catsharks, Galeus atlanticus , caught in Southern Portugal, were examined to test the validity of these two taxa. These sharks closely resemble each other, have overlapping geographical ranges and are difficult to identify by morphological characters. Non-metric multidimensional scaling of morphometric variables indicates a clear separation between the two species, with 10 characters each contributing 2·12–2·45% of the total variability between species. Maximum likelihood, parsimony and neighbour-joining trees revealed two major mtDNA haplotype clades, corresponding to the two species, with an average corrected sequence divergence between them of 3·39 ± 0·56%. Within species divergences between haplotypes averaged 0·27 ± 0·18% in G. melastomus and 0·12 ± 0·08% in G. atlanticus . A total of 35 diagnostic nucleotide site differences and four restriction fragment length polymorphism recognition sites in the ND2 gene can be used to distinguish the two species.     

Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene

Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 120 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.     

Morphological and phylogenetic analyses of <Emphasis Type="Italic">Uromyces appendiculatus</Emphasis> and <Emphasis Type="Italic">U. vignae</Emphasis> on legumes in Japan

Uromyces appendiculatus, inclusive of three varieties, is distinguished from U. vignae primarily by the position of urediniospore germ pores and putative host specificity. However, opinions concerning these morphological and physiological features as taxonomic characters have varied greatly, and distinction of these species has often been confused. To clarify the taxonomy of these two species, morphological features of urediniospores and teliospores of 225 rust fungus specimens on species of Phaseolus, Vigna, Apios, Lablab, and Dunbaria were examined by light microscopy and scanning electron microscopy. Forty-five specimens were subjected to molecular phylogenetic analyses. As a result, the position of germ pores in urediniospores and the teliospore-wall thickness were considered as good characters to separate three morphological groups. In molecular analyses, the specimens fell into two and three clades based on the nucleotide sequence at D1/D2 domain of LSU rDNA and ITS regions, respectively. One of the D1/D2 clades corresponded to one morphological group whereas another D1/D2 clade included two other morphological groups. In contrast, each of the three ITS clades corresponded to a separate morphological group. Neither morphological groups nor molecular clades were host limited. It is suggested that the three morphological groups that corresponded to three distinct ITS clades constitute distinct species.Contribution no. 186 from the Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba, Japan     

A new species of Hyphoderma (Meruliaceae, Polyporales) and its discrimination from closely related taxa

Thirty-five corticioid collections from the Canary Islands and Azores Archipelago were examined morphologically and subjected to molecular phylogenetic analysis. These specimens, almost all collected on endemic and/or xerophilic vegetation, were similar in morphological and ecological characteristics to Hypochnicium prosopidis from the Sonoran Desert (Arizona, USA) and Hyphoderma amoenum. Thirty-seven new ITS nrDNA sequences from these specimens, including the nomenclatural type of the above-mentioned species, were obtained and aligned with homologous sequences from GenBank. These collections were distributed in two strongly supported monophyletic clades. However, similar patterns of morphological variability shared by specimens included in both clades and their differences with related species suggest that they should be described as a single new species. Therefore Hyphoderma macaronesicum is proposed. Studies will be required to test, in a more robust multilocus genealogical framework, whether these populations constitute two cryptic species or whether they are the same taxon. The position of Hypochnicium prosopidis in the resolved tree and its morphological characters suggest that it should be included in Hyphoderma and the new combination Hyphoderma prosopidis is proposed.     

Phylogenetic relationships in Interfilum and Klebsormidium (Klebsormidiophyceae, Streptophyta)

Members of the genus Klebsormidium have cosmopolitan distribution and occur in a very wide range of freshwater and terrestrial habitats. Due to its simple filamentous morphology, this genus represents a taxonomically and systematically complex taxon in which phylogenetic relationships are still poorly understood. The phylogeny of Klebsormidium and closely related taxa was investigated using new ITS rRNA and rbcL sequences generated from 75 strains (isolated from field samples or obtained from culture collections). These sequences were analyzed both as single-marker datasets and in a concatenated dataset. Seven main superclades were observed in the analyses, which included sixteen well-supported clades. Some species of Klebsormidium, including the type species Klebsormidium flaccidum, were polyphyletic. Interfilum was recovered with high statistical support as sister taxon to a clade of Klebsormidium formed mainly by strains identified as K. flaccidum. Whereas some clades could be easily associated with described species, this was not possible for other clades. A new lineage of Klebsormidium, isolated from arid soils in southern Africa and comprising undescribed species, was discovered. Several morphological characters traditionally used for taxonomic purposes were found to have no phylogenetic significance and in some cases showed intra-clade variation. The capacity to form packet-like aggregates (typical of Interfilum), features of the morphology of the chloroplast and the type of habitat were the main phylogenetically relevant characters. Overall, Klebsormidium and Interfilum formed a more diverse algal group than was previously appreciated, with some lineages apparently undergoing active evolutionary radiation; in these lineages the genetic variation observed did not match the morphological and ecological diversity.     

Multigenic phylogeographic divergence in the paleoendemic southern Appalachian opilionid Fumontana deprehendor Shear (Opiliones, Laniatores, Triaenonychidae)

The paleoendemic opilionid Fumontana deprehendor is restricted to a small area of mid-elevation forested habitats in the southern Blue Ridge province of the Appalachian Mountains. In a recent study we reported on the discovery of 22 new montane populations of this monotypic genus, specimens from which exhibit remarkably little morphological divergence despite their separation by intervening lowlands and large riverine barriers. Here, we further explore spatial and temporal patterns of divergence in this taxon using DNA sequence data from a portion of the mitochondrial cytochrome c oxidase subunit I gene ( approximately 1000 bp) and full-length sequences of both nuclear ribosomal internal transcribed spacer regions, including the intervening 5.8S rRNA region ( approximately 700 bp total). Bayesian phylogenetic analyses of these independent data sets reveal congruent genealogical patterns, with all data partitioning and combination strategies consistently recovering five allopatric, geographically cohesive genetic clades. These clades show an almost complete lack of internal genetic divergence, with most individuals sharing a clade-specific, regionally widespread haplotype. The geographic distribution of these clades corresponds to patterns seen in other upland taxa of the region, possibly indicating coincident vicariance. Because of a lack of quantifiable morphological divergence and relatively modest levels of genetic divergence, we conservatively refer to the geographically cohesive genetic clades as "phylogeographic units", although these may actually represent cryptic species. Conservation implications and the prospect for future comparative arachnid phylogeography in the southern Appalachians are discussed in light of the results presented here.     

Differentiation of two hemp nettle species (Galeopsis bifida Boenn. and G. tetrahit L.) inferred from morphological characters and DNA markers

Two species of the genus Galeopsis L., G. tetrahit L. and G. bifida (family Lamiaceae), are problematic to distinguish often wrongly recognized, and treated by some taxonomists as a single species. Morphological diagnostical characters of these species are variable and partly overlap. Species independence of G. tetrahit and G. bifida was evaluated and their diagnostic characters verified using ISSR and RAPD markers. A total of 57 ISSR and 28 RAPD fragments were obtained providing distinct subdivision of the accessions examined into two groups. Analysis of molecular data using the neighbor-joining method showed that the accessions studied fell into two clades in the same way as demonstrated by the analysis of 20 morphological characters using single linkage method. The morphological characters were found to be more variable compared to the molecular markers, although the combined of these characters provided differentiation of the species.     

Small clades at the periphery of passerine morphological space

Among passerine birds (order Passeriformes), tribe- to family-level clades with five or fewer species are more frequent than one would expect from a homogeneous speciation and extinction process. Previous analyses also suggested that small clades tend to be marginal geographically and/or ecologically. In this study, I use principal component (PC) scores based on eight log-transformed measurements of the wing, tail, leg, and beak to test the hypothesis that small clades (相似文献