Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants

A widely held view of land plant relationships places liverworts as the first branch of the land plant tree, whereas some molecular analyses and a cladistic study of morphological characters indicate that hornworts are the earliest land plants. To help resolve this conflict, we used parsimony and likelihood methods to analyze a 6, 095-character data set composed of four genes (chloroplast rbcL and small-subunit rDNA from all three plant genomes) from all major land plant lineages. In all analyses, significant support was obtained for the monophyly of vascular plants, lycophytes, ferns (including PSILOTUM: and EQUISETUM:), seed plants, and angiosperms. Relationships among the three bryophyte lineages were unresolved in parsimony analyses in which all positions were included and weighted equally. However, in parsimony and likelihood analyses in which rbcL third-codon-position transitions were either excluded or downweighted (due to apparent saturation), hornworts were placed as sister to all other land plants, with mosses and liverworts jointly forming the second deepest lineage. Decay analyses and Kishino-Hasegawa tests of the third-position-excluded data set showed significant support for the hornwort-basal topology over several alternative topologies, including the commonly cited liverwort-basal topology. Among the four genes used, mitochondrial small-subunit rDNA showed the lowest homoplasy and alone recovered essentially the same topology as the multigene tree. This molecular phylogeny presents new opportunities to assess paleontological evidence and morphological innovations that occurred during the early evolution of terrestrial plants.     

Multigene analyses resolve early diverging lineages in the Rhodymeniophycidae (Florideophyceae,Rhodophyta)

Multigene phylogenetic analyses were directed at resolving the earliest divergences in the red algal subclass Rhodymeniophycidae. The inclusion of key taxa (new to science and/or previously lacking molecular data), additional sequence data (SSU, LSU, EF2, rbcL, COI‐5P), and phylogenetic analyses removing the most variable sites (site stripping) have provided resolution for the first time at these deep nodes. The earliest diverging lineage within the subclass was the enigmatic Catenellopsis oligarthra from New Zealand (Catenellopsidaceae), which is here placed in the Catenellopsidales ord. nov. In our analyses, Atractophora hypnoides was not allied with the other included Bonnemaisoniales, but resolved as sister to the Peyssonneliales, and is here assigned to Atractophoraceae fam. nov. in the Atractophorales ord. nov. Inclusion of Acrothesaurum gemellifilum gen. et sp. nov. from Tasmania has greatly improved our understanding of the Acrosymphytales, to which we assign three families, the Acrosymphytaceae, Acrothesauraceae fam. nov. and Schimmelmanniaceae fam. nov.     

Numerical and comparative analyses of the modern systems of classification of the flowering plants

The modern classifications of Cronquist, Dahlgren, Takhtajan, and Thorne have been compared with one another and also with those published at the beginning of the 20th century, which comprise the ones by Bessey, Engler, Gobi, and Hallier. Mantel and consensus tests have been used to compare the different matrices taken from the above classifications. Results indicate that all four modern classifications do not differ from one another statistically. Ordinal delimitation has not changed significantly for a century at least: Orders of the modern classifications are similar to those of the past classifications. However, the topology or structure of Cronquist’s and Takhtajan’s classifications differs from that of Bessey’s. Also, Engler’s dicotyledon classification is statistically different from those of the modern systems. Among past classifications, that of Hallier resembles the modern ones most. The resemblance among the modern classifications and, in general, with the past ones can be explained by the similarity in taxonomic principles and in the practice used. Two other factors help in explaining similarities among classifications: cognitive constraint and historical inertia. For instance, the Linnean scheme—upon which all botanical classifications are based—imposes on the latter a structure which allows only with difficulty and approximation the representation of taxon evolution. Moreover, not only have modern authors mutually influenced one another (particularly Cronquist/Takhtajan, Dahlgren/Thorne), but also they have been influenced by past authors. Indeed, modern classifications are a reshuffling of past ones. Also, Engler’s influence is great, especially at the ordinal level. For changes and modifications to become effective in future classifications of flowering plants, one will have to minimize, if not avoid, the implicit influence of the modern systems as standard systems, and to count on, among others, molecular data in redefining taxonomic concepts founded on classical morphology, and consequently to remove the prudence that makes us look at classification as a useful convention for which one of the basic criteria remains the stability of taxa recognized long ago.     

Age of the last common ancestor of extant Plasmodium parasite lineages

Parasites of the genus Plasmodium infect all classes of amniotes (mammals, birds and reptiles) and display host specificity in their infections. It is therefore generally believed that Plasmodium parasites co-evolved intimately with their hosts. Here, we report that based on an evolutionary analysis using 22 genes in the nuclear genome, extant lineages of Plasmodium parasites originated roughly in the Oligocene epoch after the emergence of their hosts. This timing on the age of the common ancestor of extant Plasmodium parasites suggest the importance of host switches and lends support to the evolutionary scenario of a "malaria big bang" that was proposed based on the evolutionary analysis using the mitochondrial genome.     

Reconstructing the ancestral female gametophyte of angiosperms: Insights from Amborella and other ancient lineages of flowering plants

For more than a century, the common ancestor of flowering plants was thought to have had a seven-celled, eight-nucleate Polygonum-type female gametophyte. It is now evident that not one, but in fact three, patterns of female gametophyte development and mature structure characterize the common ancestors of the four most ancient clades of extant angiosperms: Amborella-type, Nuphar/Schisandra-type and Polygonum-type. The Amborella-type female gametophyte is restricted to a single extant species, Amborella trichopoda, and at maturity consists of eight cells and nine nuclei. Development of the Amborella-type gametophyte is essentially identical to the Polygonum-type except that there is an additional and asynchronous cell division at the micropylar pole prior to maturation that produces a third synergid and the egg cell. The Nuphar/Schisandra-type female gametophyte is four-nucleate and four-celled and at maturity contains a typical three-celled egg apparatus and a central cell with a single haploid polar nucleus. This type of gametophyte appears to be universal among extant members of the Nymphaeales (including Hydatellaceae) and Austrobaileyales. Based on explicit reconstruction of character distribution and evolution, the Polygonum-type female gametophyte is certain to be representative of the common ancestors of monocots, eudicots, magnoliids, Ceratophyllaceae, and Chloranthaceae. There are compelling biological reasons to suggest that the four-celled, four-nucleate female gametophyte (as found in Nymphaeales and Austrobaileyales) is ancestral among angiosperms, with transitions to Polygonum-type female gametophytes separately in the Amborellales and in the ancient angiosperm clade that includes all angiosperms except Amborella, Nymphaeales, and Austrobaileyales. Subsequent to the evolution of a seven-celled, eight-nucleate Polygonum-type female gametophyte in the Amborellales, we hypothesize that a peramorphic increase in egg apparatus cell number took place and led to the unique situation in which there are three synergids in Amborella trichopoda.     

Australian native flowering plants enhance the longevity of three parasitoids of brassica pests

Floral resources from native plants that are adapted to the local environment could be more advantageous than the use of nonnative plants. In Australia, there is a dearth of information on the benefits of native plants to natural enemies and their selectivity against pests. Accordingly, we examined the longevity of the parasitoids Diaeretiella rapae (McIntosh) and Cotesia glomerata (L.) (both Hymenoptera: Braconidae), and Diadegma semiclausum (Hellen) (Hymenoptera: Ichneumonidae) exposed to flowering shoots from Australian native plants which was compared with the nonnative buckwheat (Fagopyrum esculentum), often used in conservation biological control. Longevity of parasitoids was significantly enhanced by the Australian natives Westringia fruticosa, Mentha satureioides, Callistemon citrinus, Leptospermum cv. ‘Rudolph’, Grevillea cv. ‘Bronze Rambler’, Myoporum parvifolium, Lotus australis, and nonnative F. esculentum. The highest mean survival by native plant species was 3.4× higher for D. rapae with Leptospermum sp. and 4.3× higher for D. semiclausum with M. parvifolium. For C. glomerata, Grevillea sp. increased longevity by 6.9× compared with water only. Longevity of Plutella xylostella (L.) (Lepidoptera: Plutellidae), a major crop pest, was enhanced by all plants against which it was screened except Acacia baileyana, a species that had no effect on parasitoid longevity. Several Australian native plant species that benefit parasitoids were identified. None of the plant species provided a selective benefit to the parasitoid D. semiclausum compared with its host P. xylostella; however, the benefit of M. parvifolium and Grevillea sp. on the longevity of D. semiclausum was relatively higher compared with the pest. These results suggest the need for field studies to determine whether native Australian plants increase P. xylostella impact in nearby brassica crops.     

Structural mouthpart interaction evolved already in the earliest lineages of insects

In butterflies, bees, flies and true bugs specific mouthparts are in close contact or even fused to enable piercing, sucking or sponging of particular food sources. The common phenomenon behind these mouthpart types is a complex composed of several consecutive mouthparts which structurally interact during food uptake. The single mouthparts are thus only functional in conjunction with other adjacent mouthparts, which is fundamentally different to biting–chewing. It is, however, unclear when structural mouthpart interaction (SMI) evolved since this principle obviously occurred multiple times independently in several extant and extinct winged insect groups. Here, we report a new type of SMI in two of the earliest wingless hexapod lineages—Diplura and Collembola. We found that the mandible and maxilla interact with each other via an articulatory stud at the dorsal side of the maxillary stipes, and they are furthermore supported by structures of the hypopharynx and head capsule. These interactions are crucial stabilizing elements during food uptake. The presence of SMI in these ancestrally wingless insects, and its absence in those crustacean groups probably ancestral to insects, indicates that SMI is a groundplan apomorphy of insects. Our results thus contradict the currently established view of insect mouthpart evolution that biting–chewing mouthparts without any form of SMI are the ancestral configuration. Furthermore, SMIs occur in the earliest insects in a high anatomical variety. SMIs in stemgroup representatives of insects may have triggered efficient exploitation and fast adaptation to new terrestrial food sources much earlier than previously supposed.     

Geometric morphometric analyses of worn cheek teeth help identify extant and extinct gophers (Rodentia,Geomyidae)

Studies of the biostratigraphy and palaeoecology of fossil vertebrate assemblages require large samples of accurately identified specimens. Such analyses can be hampered by the inability to assign isolated and worn remains to specific taxa. Entoptychine gophers are a diverse group of burrowing rodents found in Oligo‐Miocene deposits of the western United States. In both entoptychines and their extant relatives the geomyines, diagnostic characters of the occlusal surface of the teeth are modified with wear, making difficult the identification of many isolated fossil teeth. We use geometric morphometrics to test the hypothesis that tooth shape informs taxonomic affinities and expected levels of morphological variation across gopher taxa. We also incorporate data from microcomputer tomography to investigate changes in occlusal surface shape through wear within individuals. Our analyses demonstrate the usefulness of our approach in identifying extant geomyines to the genus, subgenus and species levels, and fossil entoptychines to the genus and, in some cases, the species level. Our results cast doubt on the validity of some species within Entoptychus and suggest future revisions to entoptychine taxonomy. The amounts of morphological divergence observed among fossil and extant genera are similar. Fossil species do not differ greatly from extant ones in that regard either. Further work evaluating the morphological variation within and across entoptychine species, including unworn teeth and osteological material, will allow revised analyses of the biostratigraphy and palaeoecology of important Oligo‐Miocene mammalian assemblages of the western United States and help to infer the phylogenetic relationships and evolution of gophers.     

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

We report on two new lineages of the Eumida sanguinea complex from Great Britain and describe one of them as a new species using a multilocus approach, including the mitochondrial DNA COI-5P and the nuclear markers ITS (ITS1, 5.8S rRNA and ITS2) and 28S rRNA. The molecular analysis placed Eumida mackiei sp. nov. in a monophyletic clade with 19.1% (COI), 10.1% (ITS) and 1.7% (28S) mean distance to its nearest neighbour. Molecular diagnoses were also applied to nine lineages within the E. sanguinea complex. This was complemented with morphometric data employing multivariate statistical analysis and the incorporation of statistical dissimilarities against three other described species from the complex. Eumida mackiei sp. nov. can be distinguished from E. notata and E. maia by the larger distance between the eyes and differences in morphometric proportions mainly in the dorsal and ventral cirri as well as in the prostomial appendages. E. sanguinea sensu stricto failed to produce a cluster of its own in the morphometric analysis, probably due to juvenile bias. Integrative taxonomy provided strong evidence to formally describe a new cryptic species that can now be used in biomonitoring or other relevant ecological research.     

Combined molecular and morphological evidence on the phylogeny of the earliest lepidopteran lineages

Agreement among recent morphological and molecular phylogenetic analyses has strengthened estimates of the relationships among the earliest lineages of the holometabolan order Lepidoptera. For a few major groups, evidence for monophyly and basal relationships remains relatively weak or contradictory — chiefly within the clades of basal Glossata and Heteroneura. Here we assess the support for these controversial areas of lepidopteran classification through molecular systematic investigation of 18S rDNA sequence variation. Parsimony and maximum likelihood analyses are presented for 1379 alignable sites of 18S. These data are then combined with 61 morphological features scored for major lineages of basal Glossata and Heteroneura. Our 18S rDNA data support recent hypotheses for the placement of Micropterigidae and Agathiphagidae as the basal-most lineages of Lepidoptera, and support the monophyly of the groups Neolepidoptera and Exoporia. 18S data alone are shown to be insufficient for resolving the monophyly and relationships of the Glossata, and for specifying relationships above the Neolepidoptera. Combination of the 18S data with published morphological ground-plan scorings improves overall support for the morphology-based hypothesis for basal glossatans, but phylogenetic resolution among published alternatives for the basal Heteroneura remains a major question for lepidopteran systematics.     

Phylogeny and classification of the extant basal lineages of the Hymenoptera (Insecta)

The phylogeny of the basal hymenopteran lineages, including representatives of all ‘symphytan’ families, is anal; In total, 236 morphological characters were scored for 44 exemplars, including six outgroup, two xyelic tenthredinoid, five pamphilioid, three cephoid, five ‘siricoid’, one orussid, and six apocritan taxa. The datas analysed with parsimony under equal weights and under implied weights. The monophyly of the Hymenopte strongly supported but the sistergroup of the Hymenoptera cannot be identified with confidence. The relations of the ‘symphytan’ lineages are Xyeloidea +(Tenthredinoidea+ (Pamphilioidea + (Cephoidea + (Ariaxyelic (Siricidae + (Xiphydriidae +(Orussoidea+Apocrita))))))). Many of the relationships between the superfamilies, especially in the basal branching pattern, are only weakly corroborated. The monophyly of most superfamilies is supported, and all may be monophyletic except the ‘Siricoidea’, which is clearly paraphyletic. It is difficult to di whether the Siricidae or the Anaxyelidae are the closest relatives of Xiphydriidae + (Orussoidea + Apocrita). support for the sistergroup relationship between the Orussoidea and the Apocrita is substantial, putative apomorphies being provided by most character systems. There is also good evidence in favour of the monophj the Apocrita. The internal phylogeny of the Tenthredinoidea differs considerably from the results of earlier anal The Blasticotomidae are the sistergroup of the Tenthredinoidea s.s. Relationships at the base of the Tenthredini s.s. are weakly supported. It is uncertain whether the Tenthredinidae are monophyletic or comprise a 1 paraphyletic grade within the Tenthredinoidea s.s. The Diprionidae may be the sistergroup to Cimbicidae +(Argidae+ Pergidae). Most relationships within the Cimbicidae + (Argidae + Pergidae) clade are corroborated, with the exception of the monophyly of the Argidae. It is proposed to elevate the Anaxyelidae the Xiphydriida both to superfamily status. The family‐level classification of the Tenthredinoidea will probably have to be changed, but this must await further clarification of the phylogeny of this superfamily.     

Subunit structure of three glyceraldehyde 3-phosphate dehydrogenases of some flowering plants.

A procedure is described for the purification of three glyceraldehyde phosphate dehydrogenases from a batch of beet leaves. Glyceraldehyde 3-phosphate:NADP⁺ reductase, nonphosphorylating (EC 1.2.1.9) has been purified over 1500-fold. The M_r of this enzyme is 190,000 and its subunits have an M_r of 53,000, suggesting a tetramer as the active form. Its pI is 6.0. Cytosolic glyceraldehyde 3-phosphate dehydrogenase, NAD dependent (EC 1.2.1.12), has an M_r of 145,000 and subunits of M_r 37,000. It is dissociated to inactive dimers by ATP, whereas NAD⁺ in the presence of reductant promotes its reactivation. The amino acid composition is related to glyceraldehyde 3-phosphate dehydrogenases from animal sources and is most similar to pea seed glyceraldehyde 3-phosphate dehydrogenase. The enzyme exhibits a range of pI values from 5 to 7, but a second electrofocusing in the presence of dithioerythritol results in a single main form with pI 5.33, consistent with the behavior in polyacrylamide and cellulose acetate gel electrophoresis. Chloroplast NAD(P)-glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.13) has been obtained from beet, pea, Ranunculus, Arum, and maize leaves. The stable form is an oligomer of about 800,000 M_r (±10%), while a minor, possibly damaged fraction elutes as a retarded peak from agarose columns. The M_r 800,000 form is reversibly dissociated to protomers of M_r 160,000 by NADP⁺, with increase of apparent NADP-dependent activity. Two subunits are present in similar amounts in all association states and after all treatments: α with M_r 36,000, and β with M_r 41,000. The form found in density gradient ultracentrifugation has an M_r of 390,000. Isoelectric points of the various forms lie between pH 4.1 and 4.7 for all species, with a main peak usually at pI 4.45. The amino acid composition of beet chloroplast glyceraldehyde phosphate dehydrogenase is not closely related to that of beet leaf NAD-dependent glyceraldehyde 3-phosphate dehydrogenase.     

Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations

Analysis of 12 polymorphic simple sequence repeats identified in the genome sequence of Phytophthora ramorum, causal agent of 'sudden oak death', revealed genotypic diversity to be significantly higher in nurseries (91% of total) than in forests (18% of total). Our analysis identified only two closely related genotypes in US forests, while the genetic structure of populations from European nurseries was of intermediate complexity, including multiple, closely related genotypes. Multilocus analysis determined populations in US forests reproduce clonally and are likely descendants of a single introduced individual. The 151 isolates analysed clustered in three clades. US forest and European nursery isolates clustered into two distinct clades, while one isolate from a US nursery belonged to a third novel clade. The combined microsatellite, sequencing and morphological analyses suggest the three clades represent distinct evolutionary lineages. All three clades were identified in some US nurseries, emphasizing the role of commercial plant trade in the movement of this pathogen.     

Universal hydraulics of the flowering plants: vessel diameter scales with stem length across angiosperm lineages,habits and climates

Angiosperm hydraulic performance is crucially affected by the diameters of vessels, the water conducting conduits in the wood. Hydraulic optimality models suggest that vessels should widen predictably from stem tip to base, buffering hydrodynamic resistance accruing as stems, and therefore conductive path, increase in length. Data from 257 species (609 samples) show that vessels widen as predicted with distance from the stem apex across angiosperm orders, habits and habitats. Standardising for stem length, vessels are only slightly wider in warm/moist climates and in lianas, showing that, rather than climate or habit, plant size is by far the main driver of global variation in mean vessel diameter. Terminal twig vessels become wider as plant height increases, while vessel density decreases slightly less than expected tip to base. These patterns lead to testable predictions regarding evolutionary strategies allowing plants to minimise carbon costs per unit leaf area even as height increases.     

Nucleotide sequence analyses of the cytoplasmic 5S ribosomal ribonucleic acid from five species of flowering plants

Broad-bean 5S rRNA labelled with (32)P was digested separately with T(1) and pancreatic A ribonucleases and the resulting oligonucleotides (20 and 18 respectively) were fractionated by two-dimensional electrophoresis. The oligonucleotides were analysed further and 32 of them have been completely sequenced. They were compared with those of 5S rRNA from dwarf bean, sunflower, tomato and rye. Sequence differences were found at both the 3'- and 5'-termini and at up to nine other positions. Most base substitutions were transitions between C and U. In common with other 5S rRNA species that have been analysed the ends of the molecule in each plant species have complementary sequences.     

Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans

Relationships among and within baleen and toothed whales were examined using the complete sequence of the mitochondrial cytochrome b gene. Based on parsimony analyses of conservative nucleotide substitutions, five primary evolutionary lineages of extant cetaceans were identified, one represented by baleen whales (Mysticeti) and four represented by odontocetes (toothed whales). Based on the most comprehensive representation of taxa, both cetaceans and artiodactyls, the most parsimonious relationship among the five lineages is (Mysticeti, Odontoceti (Platanistoidea (Physeteroidea (Ziphioidea (Delphinida))))). This relationship, however, is labile and sensitive to ingroup representation and the choice of outgroup. The short nodes among the five cetacean lineages suggest that the divergence among these lineages occurred over a narrow time period, a finding consistent with the limited fossil evidence that indicates a major cetacean radiation 30-34 Mya. The level of divergence among the five cetacean lineages, and that seen between cetaceans and artiodactyls, suggests that cetaceans and artiodactyls had a common ancestor approximately 60 Mya.