Molecular phylogeny of the Acre clade (Crassulaceae): Dealing with the lack of definitions for Echeveria and Sedum

The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the “Acre clade”, a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European–Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera – Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences

This study investigates the molecular phylogeny of seven lionfishes of the genera Dendrochirus and Pterois. MP, ML, and NJ phylogenetic analysis based on 964 bp of partial mitochondrial DNA sequences (cytochrome b and 16S rDNA) revealed two main clades: (1) “Pterois” clade (Pterois miles and Pterois volitans), and (2) “Pteropterus–Dendrochirus” clade (remainder of the sampled species). The position of Dendrochirus brachypterus either basal to the main clades or in the “Pteropterus–Dendrochirus” clade cannot be resolved. However, the molecular phylogeny did not support the current separation of the genera Pterois and Dendrochirus. The siblings P. miles and P. volitans are clearly separated and our results support the proposed allopatric or parapatric distribution in the Indian and Pacific Ocean. However, the present analysis cannot reveal if P. miles and P. volitans are separate species or two populations of a single species, because the observed separation in different clades can be either explained by speciation or lineage sorting. Molecular clock estimates for the siblings P. miles and P. volitans suggest a divergence time of 2.4–8.3 mya, which coincide with geological events that created vicariance between populations of the Indian and Pacific Ocean.     

The Phylogenetics of Mycotoxin and Sclerotium Production in Aspergillus flavus and Aspergillus oryzae

Aspergillus flavus is a common filamentous fungus that produces aflatoxins and presents a major threat to agriculture and human health. Previous phylogenetic studies of A. flavus have shown that it consists of two subgroups, called groups I and II, and morphological studies indicated that it consists of two morphological groups based on sclerotium size, called “S” and “L.” The industrially important non-aflatoxin-producing fungus A. oryzae is nested within group I. Three different gene regions, including part of a gene involved in aflatoxin biosynthesis (omt12), were sequenced in 33 S and L strains of A. flavus collected from various regions around the world, along with three isolates of A. oryzae and two isolates of A. parasiticus that were used as outgroups. The production of B and G aflatoxins and cyclopiazonic acid was analyzed in the A. flavus isolates, and each isolate was identified as “S” or “L” based on sclerotium size. Phylogenetic analysis of all three genes confirmed the inference that group I and group II represent a deep divergence within A. flavus. Most group I strains produced B aflatoxins to some degree, and none produced G aflatoxins. Four of six group II strains produced both B and G aflatoxins. All group II isolates were of the “S” sclerotium phenotype, whereas group I strains consisted of both “S” and “L” isolates. Based on the omt12 gene region, phylogenetic structure in sclerotium phenotype and aflatoxin production was evident within group I. Some non-aflatoxin-producing isolates of group I had an omt12 allele that was identical to that found in isolates of A. oryzae.     

On necessary and sufficient conditions for group selection efficacy

The statement “group selection predominates over individual selection” is formulated within a class of patch-structured models. Conditions involving both “selfish” and “altruistic” predator characteristics are then shown to be necessary and sufficient for group selection predominance in this class of models. Maynard Smith's criterion M < 1 (Group selection, Quart. Rev. Biol., June 1976, pp. 277–283) is shown to be sufficient but not necessary for group selection predominance.     

The seashore sedges of the Russian Kola Peninsula: How many species?

A necessary basis for environmental protection is thorough knowledge of the biodiversity to be protected. Setting conservation priorities in taxonomically complex groups is an especially difficult task. The seashore sedges of the Carex salina group (Cyperaceae) of the Russian White and Barents Seas form important parts of the coastal ecosystems and include species listed as rare and endangered. However, their taxonomy is poorly understood and supposed to be blurred by hybridization, also including the closely related C. aquatilis and possibly other species of sect. Phacocystis (C. bigelowii, C. nigra s. lat.). We address the taxonomic situation in the C. salina group in the Kola Peninsula with emphasis on taxa of supposed hybrid origin (C. salina and C. recta coll.). We analyzed 92 plants from 28 sites for 101 amplified fragment length polymorphisms (AFLPs) and 10 morphological characters. The plants referred to three supposedly “pure” species (C. aquatilis, C. paleacea and C. subspathacea) formed different extreme parts of the morphological and molecular variation. These species could be discriminated by a combination of morphological characters. The two taxa of proposed hybrid origin had extremely variable morphology and could not be clearly distinguished from each other or from the supposedly “pure” species. Our results demonstrate extensive gene flow between all taxa, suggesting that the entire C. salina group including C. aquatilis acts as a single large biological species.     

Molecular Phylogeny and Systematics of Anoplocephaline Cestodes in Rodents and Lagomorphs

A molecular phylogenetic hypothesis is presented for the anoplocephaline cestodes of placental mammals based on sequence data from the mitochondrial cytochrome c oxidase I (COI) gene, the nuclear-encoded 28S rRNA gene and the internal transcribed spacer region I of rRNA (ITS1). The material consists of 35 species representing nine genera of cestodes, with emphasis on taxa parasitising rodents and lagomorphs in the Holarctic region. The resulting phylogenies show considerable disagreement with earlier systematic and phylogenetic hypotheses derived from morphology. Specifically, the results contradict the view of uterine morphology being the primary determinant of deeper phylogenetic splits within Anoplocephalinae. Also, the role of genital duplication as a means of generic divergence was not found to follow consistently the pattern suggested by earlier hypotheses. Colonisation of novel host lineages has evidently been the predominant mode of diversification in anoplocephaline cestodes of placental mammals; evidence for phyletic co-evolution was obscure. The phylogenies consistently distinguished a large monophyletic group including all species from arvicoline rodents (voles and lemmings), primarily representing the genera Anoplocephaloides Baer, 1923 and Paranoplocephala Lühe, 1910. Phylogenetic relationships within the “arvicoline clade” of cestodes were generally poorly resolved. Consistent support for nodes above and below the unresolved polytomy indicates a rapid radiation involving a nearly simultaneous diversification of many lineages, a scenario also proposed for the arvicoline hosts.     

Cambrian view

The analysis of visual systems is a valuable method of assessing phylogenetic processes. As in the present animal world, we find simple and complex systems in the Lower Cambrian. One may detect “simple eyes” for example with an advanced design in lobopodians, while the existence of even more simple “simple eyes” is very probable but still to be proved. More complex systems are to be found. In Leanchoilia illecebrosa Hou, 1987 and Leanchoilia superlata Walcott, 1912 there are probable dorsal median eyes and a pair of fine, stalked ventral eyes. Both systems may contribute to phylogenetic and systematic discussions. These presumably movable stalked eyes may be regarded as an adaptation to a mobile lifestyle. They suggest that the physiologic principle of nystagmus to stabilise the visual world of an animal in motion was already realised in Leanchoilia, perhaps for the first time. To analyse the surface of the early eyes from the Lower Cambrian – not only of Leanchoilia, but of any other forms as well – the number, shape and other parameters of the lenses could lead to further knowledge regarding vision in early invertebrates.     

Lower Cretaceous benthic foraminifera from DSDP Site 263: micropalaeontological constraints for the early evolution of the Indian Ocean

Analysis of 66 samples from DSDP Site 263 (Cores 263-4R-4 to 263-29R-4) reveals a unique faunal composition with a predominance of agglutinated taxa, many of them previously unrecorded from any other DSDP and ODP Indian Ocean sites. A total of 66 agglutinated and 31 calcareous taxa are documented and five new species are described: Hippocrepina gracilis n.sp., “Textulariopsis” elegans n.sp., Aaptotoichus challengeri n.sp., “Gaudryinopsis” pseudobettenstaedti n.sp. and “Gaudryina” cuvierensis n.sp. Three assemblages are recognized based on changes in the composition of dominant taxa and occurrences of stratigraphically important species: (1) a high-diversity Valanginian to Barremian Bulbobaculites-Recurvoides Assemblage (Cores 263-29R to -18R), comprised of numerous elongate agglutinated forms, rare nodosariids, and variable numbers of tubes and ammodiscids; (2) a moderately diverse Aptian to Albian Rhizammina-Ammodiscus-Glomospira Assemblage (Cores 26318R to -7R) with highly fluctuating numbers of the nominate taxa and Haplophragmoides, Trochammina, Verneuilinoides spp., and Vemeuilina howchini; (3) a very low diversity Albian or younger Assemblage (Cores 263-6R to -4R) containing sparse agglutinated foraminifera, rare nodosariids and rotaliids. We interpret the assemblages as shelf to lower slope and consider them to reflect a deepening palaeobathymetry as the Cuvier margin subsided after the initial breakup of East Gondwana during the Valanginian. Our interpretation is in sharp contrast with initial palaeodepth estimates of less than 100 m, as well as with original chronostratigraphic interpretations based on foraminifera and nannofossils which correlated the base of the recovered interval with the Aptian. The absence of many cosmoplitan forms, despite high diversity, suggests strong faunal differentiation in the Austral realm or endemisn within the Cuvier Basin during the Early Cretaceous.     

End of season carbon supply status of woody species near the treeline in western China

As trees and shrubs approach the high elevation tree limit, it is often assumed that they fall short in photosynthate (source limitation). Alternatively, low temperature may restrict carbon investment (growth, sink limitation). The content of mobile non-structural carbohydrates (NSC) in tissues is considered a measure of the carbon source–sink balance. To test the source vs. sink limitation hypothesis, we compared late-season NSC concentrations of various woody taxa across altitudinal gradients from the subalpine forest to the treeline at the eastern edge of the Tibetan Plateau. Since we were interested in the generality of trends, we present “community” trends across four taxa, namely Quercus aquifolioides, Abies faxoniana, Rhododendron fabri subsp. prattii and Sorbus rufopilosa. NSC concentrations increased significantly with altitude in branch wood, current-year and last-year leaves, while there were no significant trends in stem sapwood and root xylem. The sugar to starch ratio was roughly 1:1 in branches and evergreen leaves, while stems and roots showed a higher starch fraction. Analyses of total nitrogen in leaves and wood tissues indicated no change in the trees’ nitrogen supply with elevation. The overall altitudinal trends of NSC in this group of woody plant species revealed no depletion of carbon reserves near the tree limit, suggesting that sink limitation predominates woody plant life across this treeline ecotone community.     

The phylogeny of the genus Ischioscia Verhoeff, 1928, with redescriptions of three species (Crustacea: Isopoda: Oniscidea)

The genus Ischioscia Verhoeff, 1928 is reviewed. 26 species are considered valid. A key for their identification is given, as well as a map showing the geographic distribution. The known range of the genus covers a large area from the central Amazon region to the mountains of Guatemala. The species of Ischioscia have a typical “philosciid” habitus (“runner” type); they can be distinguished from other Neotropical species with similar habitus by the following apomorphies: (1) male pereiopod 1 carpus enlarged to a plate-like extension, (2) scale field on male pereiopod 1 covering entire frontal side of the carpus, (3) male pereiopod 7 ischium with a ventral scale field, (4) dactylus in both sexes with a long inner claw. The groundpattern of Ischioscia is reconstructed, and an analysis of the phylogenetic relations within the genus is made on the basis of morphological data. The species are very similar to each other, most differences are found in the male structures of sexually dimorphic features. Ischioscia sturmi (Vandel, 1972), I. amazonica Lemos de Castro, 1955 and I. bolivari Vandel, 1968 are redescribed in detail.     

Reconsideration of systematic relationships within the order Euplotida (Protista, Ciliophora) using new sequences of the gene coding for small-subunit rRNA and testing the use of combined data sets to construct phylogenies of the Diophrys-complex

Comprehensive molecular analyses of phylogenetic relationships within euplotid ciliates are relatively rare, and the relationships among some families remain questionable. We performed phylogenetic analyses of the order Euplotida based on new sequences of the gene coding for small-subunit RNA (SSrRNA) from a variety of taxa across the entire order as well as sequences from some of these taxa of other genes (ITS1-5.8S-ITS2 region and histone H4) that have not been included in previous analyses. Phylogenetic trees based on SSrRNA gene sequences constructed with four different methods had a consistent branching pattern that included the following features: (1) the “typical” euplotids comprised a paraphyletic assemblage composed of two divergent clades (family Uronychiidae and families Euplotidae–Certesiidae–Aspidiscidae–Gastrocirrhidae), (2) in the family Uronychiidae, the genera Uronychia and Paradiophrys formed a clearly outlined, well-supported clade that seemed to be rather divergent from Diophrys and Diophryopsis, suggesting that the Diophrys-complex may have had a longer and more separate evolutionary history than previously supposed, (3) inclusion of 12 new SSrRNA sequences in analyses of Euplotidae revealed two new clades of species within the family and cast additional doubt on the present classification of genera within the family, and (4) the intraspecific divergence among five species of Aspidisca was far greater than those of closely related genera. The ITS1-5.8S-ITS2 coding regions and partial histone H4 genes of six morphospecies in the Diophrys-complex were sequenced along with their SSrRNA genes and used to compare phylogenies constructed from single data sets to those constructed from combined sets. Results indicated that combined analyses could be used to construct more reliable, less ambiguous phylogenies of complex groups like the order Euplotida, because they provide a greater amount and diversity of information.     

The nature and affinities of the “robust” Australopithecines: a review

The fossil evidence of the “robust” australopithecines is reviewed with an emphasis on the taxonomic divisions and evolutionary relationships among this group of hominids. The hypodigms of A. robustus, A. crassidens and A. boisei are described, and the significance of morphological variation within and between these species is assessed. Phylogenetic relationships among the “robust” australopithecines are examined using maximum parsimony analysis, and evolutionary scenarios are evaluated in the light of recent discoveries in East Africa.     

On the interaction between stabilizing social factors and destabilizing trophic factors in small rodent populations

Mathematical models are developed in order to analyze whether or not social factors, such as, for example, the “social fence” (J. B. Hestbeck, 1982, Oikos 39, 157–163) will stabilize population density: the dynamic interaction between social factors and (dynamic) trophic factors is analyzed. It is concluded that social factors such as the “social fence” tend to stabilize population density; hence, if density cycles (as, e.g., seen in many microtine rodents) are observed in nature, it seems reasonable to conclude that density cycles are driven by, for example, trophic interactions and not by social factors. It is suggested that the “social fence” may explain why so many populations including several microtine populations have fairly stable densities despite the ever-existing destabilizing trophic interactions. Contrary to what is implied by J. B. Hestbeck (1983, “A Mathematical Model of Population Regulation in Cyclic Mammals,” Lecture notes in biomathematics, Vol. 52, Springer-Verlag, Berlin/New York), the analysis presented in this paper demonstrates that seasonal environmental changes are not essential for the generation of regular density cycles. Seasonal changes may, however, be necessary for generating a microtine-like density cycle. Empirical information on microtine rodents relating to the “social fence hypothesis” is discussed.     

Pleosporales in Japan (5): Pleomassaria, Asteromassaria, and Splanchnonema

Eight species in Pleomassariaceae are described and illustrated. They are Pleomassaria maxima, Pl. swidae, Pl. siparia “type A,” Prosthemium canba, Asteromassaria macroconidica, A. pulchra, Splanchnonema mori, and S. argus. Of these, Pl. swidae on twigs of Swida controversa, Pr. canba on Betula ermanii, and A. macroconidica on twigs of Prunus ×yedoensis and an unknown woody plant are new. Three species, Pl. siparia “type A,” A. pulchra, and S. argus, are reported from Japan for the first time. A new combination, S. mori (≡ Massaria mori), is proposed.     

Evolutionary Assembly of the Milkweed Fauna: Cytochrome Oxidase I and the Age of TetraopesBeetles

The insects that feed on the related plant families Apocynaceae and Asclepiadaceae (here collectively termed “milkweeds”) comprise a “component community” of highly specialized, distinctive lineages of species that frequently sequester toxic cardiac glycosides from their host plants for defense against predators and are thus often aposematic, advertising their consequent unpalatability. Such sets of specialized lineages provide opportunities for comparative studies of the rate of adaptation, diversification, and habitat-related effects on molecular evolution. The cerambycid genus Tetraopes is the most diverse of the new world milkweed herbivores and the species are generally host specific, being restricted to single, different species of Asclepias, more often so than most other milkweed insects. Previous work revealed correspondence between the phylogeny of these beetles and that of their hosts. The present study provides analyses of near-complete DNA sequences for Tetraopes and relatives that are used to establish a molecular clock and temporal framework for Tetraopes evolution with their milkweed hosts.     

“Action potentials” in NEUROSPORA CRASSA, a mycelial fungus

Occasional spontaneous “action potentiais” are found in mature hyphae of the fungus Neurospora crassa. They can arise either from low-level sinusoidal oscillations of the membrane potential or from a linear slow depolarization which accelerates into a rapid upstroke at a voltage 5–20 mV depolarized from the normal resting potential (near − 180 mV). The “action potentiais” are long-lasting, 1–2 min and at the peak reach a membrane potential near −40 mV. A 2− to 8−fold increase of membrane conductance accompanies the main depolarization, but a slight decrease of membrane conductance occurs during the slow depolarization. Two plausible mechanisms for the phenomenon are (a) periodic increases of membrane permeability to inorganic ions, particularly H⁺ or Cl^- and (b) periodic decreases in activity of the major electrogenic pump (H⁺) of the Neurospora membrane, coupled with a nonlinear (inverse sigmoid) current-voltage relationship.Identification of action potential-like disturbances in fungi means that such behavior has now been found in all major biologic taxa which have been probed with suitable electrodes. As yet there is no obvious function for the events in fungi.     

Artinskian–Wordian antitropical rugose coral associations: A palaeogeographical approach

Recent investigations in the Urals and East-European Platform as well as study of corals collections from South Primorye (Russian Far East) and South-Eastern Pamirs have been undertaken. Antitropical rugose associations include taxa that are bounded in their distribution by the temperate zones of the Boreal and Perigondwanan realms. They occur sporadically in tropical latitudes but never form abundant and diverse communities. Antitropical associations are represented by the so-called ‘Cyathaxonia fauna’ (sensu lato), predominating in two selected stratigraphic intervals. The abrupt change of taxonomic composition from colonial to ‘Cyathaxonia fauna’ allows the separation of two assemblages: (i) mid Artinskian–Kungurian and (ii) Roadian–Wordian. The key regions for comparison are the Urals (mid Artinskian–Kungurian), Spitsbergen (Kungurian–Wordian), East-European Platform (Roadian), Texas (mid Artinskian–Kungurian), South Primorye (Wordian–Capitanian), South-Eastern Pamirs (Upper Artinskian), and the Sverdrup Basin (Wordian). The Late Artinskian fauna of the South-Eastern Pamirs and Wordian faunas of South Primorye bear features of mixed assemblages. A few models of the origination of antitropical assemblages are acceptable: (i) the convergent parallel evolution of Lophophyllidium in the Northern Hemisphere and Southern Hemisphere, (ii) a similar evolution trend developed in parallel in three geographically distant regions: Verbeekiella, Pseudowannerophyllum, and “Pseudoverbeekiella”, and (iii) immigration of some species within temperate zones caused by current circulation changes both in the Northern and Southern Hemispheres, as well as northward spreading of terranes in the Perigondwanan Realm.     

Stigmariopsis, Stigmaria asiatica, and the survival of the Sigillaria brardii-ichthyolepis group in the tropics of the late Pennsylvanian and Early Permian

Stigmaria asiatica Jongmans et Gothan was discovered in situ in a volcanic tuff layer between two coal seams in the lowermost Permian rocks of the Wuda coal district in Inner Mongolia, China. The species is characterized by its consistently small axial width of 20–30 mm and the combination of vertical and horizontal orientation of each axis. It is interpreted as being attached below the stigmarian axes of trees of the Sigillaria brardii-ichthyolepis group forming a deeper reaching “stigmariopsid” system. Such a unique two-tier rooting system gave this group advantages over other arboreous (tree-sized) lycopsids of the late Palaeozoic. Trees of the S. brardii-ichthyolepis group could reach deeper water resources and thus survive in wetlands that experienced dry seasons with a lowered water table. This complex underground rooting system appears to be one factor that enabled this group to survive the regional extirpation of arboreous lycopsids at the Moscovian–Kasimovian boundary in Euramerica and at the same time be a major peat-forming plant in Cathaysia.