Phylogeny of the genus Arenavirus

The family Arenaviridae consists of a unique genus (Arenavirus) that currently comprises 22 viral species, as recognized by the International Committee for Taxonomy of Viruses. Seven newly discovered represent putative new species. Here, our aims were to provide the most comprehensive phylogenetic analysis of members and putative members of the family Arenaviridae to date, and to investigate the genetic diversity observed within and between recognized species of New world arenaviruses to determine whether the genetic criteria previously proposed to define arenavirus species for Old world arenaviruses should be retained or are more widely applicable to the whole genus.     

Phylogeny and taxonomy of the genus Cylindrocladiella

The genus Cylindrocladiella was established to accommodate Cylindrocladium-like fungi that have small, cylindrical conidia and aseptate stipe extensions. Contemporary taxonomic studies of these fungi have relied on morphology and to a lesser extent on DNA sequence comparisons of the internal transcribed spacer regions (ITS 1, 2 and 5.8S gene) of the ribosomal RNA and the ??-tubulin gene regions. In the present study, the identity of several Cylindrocladiella isolates collected over two decades was determined using morphology and phylogenetic inference. A phylogeny constructed for these isolates employing the ??-tubulin, histone H3, ITS, 28S large subunit and translation elongation factor 1-alpha gene regions resulted in the identification of several cryptic species in the genus. In spite of the 18 new Cylindrocladiella species described in this study based on morphological and sequence data, several species complexes remain unresolved.     

Insect-like olfactory adaptations in the terrestrial giant robber crab

The robber crab (Birgus latro), also known as the coconut crab, is the world's largest land-living arthropod, with a weight reaching 4 kg and a length of over half a meter [1]. Apart from the marine larval stage 2, 3, this crab is fully terrestrial, and will actually drown if submerged in water [4]. A transition from sea to land raises dramatically new demands on the sensory equipment of an animal. In olfaction, the stimulus changes from hydrophilic molecules in aqueous solution to mainly hydrophobic in the gaseous phase [5]. The olfactory system of land crabs thus represents an excellent opportunity for investigating the effects of the transition from sea to land. Have land crabs come to the same solutions as other terrestrial animals, or is their olfactory sense characterized by unique innovations? Here, we show that the robber crab has evolved an olfactory sense with a high degree of resemblance to the insect system. The similarities extend to physiological, behavioral, and morphological characters. The insect nose of the robber crab is a striking example of convergent evolution and nicely illustrates how similar selection pressures result in similar adaptation     

Kinematics of the cercopithecine foot on arboreal and terrestrial substrates with implications for the interpretation of hominid terrestrial adaptations

The stereotyped characterizations of quadrupedal foot postures were tested by examining the kinematics of the cercopithecine foot on arboreal and terrestrial supports. Strictly arboreal species were compared with semi-terrestrial species for Cercopithecus, Cercocebus, Lophocebus, and Papio, in semi-natural or experimental settings. Results indicate that the kinematics of the cercopithecine arboreal quadruped differ in degree from stereotypical expectations for an arboreal quadruped. The relatively extended, adducted limb movements of the cercopithecines and the emphasis on the central digit as the functional axis of the foot suggest convergence with terrestrial mammalian cursors, and differ from the platyrrhine or colobine arboreal quadruped. The characteristics of the quadrupedal terrestrial primate foot contrast with the very unique pattern seen in the hominid foot. These contrasts provide a new perspective from which to interpret the hominid adaptation, in which the functional axis has remained fixed between the first and second digits. This pattern differs from virtually all other terrestrial mammals. The influence of bipedalism on this functional pattern is examined.     

Photoreceptor spectral sensitivities in terrestrial animals: adaptations for luminance and colour vision

This review outlines how eyes of terrestrial vertebrates and insects meet the competing requirements of coding both spatial and spectral information. There is no unique solution to this problem. Thus, mammals and honeybees use their long-wavelength receptors for both achromatic (luminance) and colour vision, whereas flies and birds probably use separate sets of photoreceptors for the two purposes. In particular, we look at spectral tuning and diversification among 'long-wavelength' receptors (sensitivity maxima at greater than 500 nm), which play a primary role in luminance vision. Data on spectral sensitivities and phylogeny of visual photopigments can be incorporated into theoretical models to suggest how eyes are adapted to coding natural stimuli. Models indicate, for example, that animal colour vision--involving five or fewer broadly tuned receptors--is well matched to most natural spectra. We can also predict that the particular objects of interest and signal-to-noise ratios will affect the optimal eye design. Nonetheless, it remains difficult to account for the adaptive significance of features such as co-expression of photopigments in single receptors, variation in spectral sensitivities of mammalian L-cone pigments and the diversification of long-wavelength receptors that has occurred in several terrestrial lineages.     

Phylogeny of the mega-diverse Gelechioidea (Lepidoptera): adaptations and determinants of success

The Gelechioidea, with 18,000 described and many more unnamed species ranks among the most diverse lepidopteran superfamilies. Nevertheless, their taxonomy has remained largely unresolved, and phylogenetic affinities among gelechioid families and lower taxa have been insufficiently understood. We constructed, for the first time, a comprehensive molecular phylogeny for the Gelechioidea. We sampled seven genes, in total 5466 base pairs, of 109 gelechioid taxa representing 32 of 37 recognized subfamilies, and two outgroup taxa. We used maximum likelihood methods and Bayesian inference to construct phylogenetic trees. We found that the families Autostichidae, Lecithoceridae, Xyloryctidae, and Oecophoridae s. str., in this order, are the most basally arising clades. Elachistidae s. l. was found to be paraphyletic, with families such as Gelechiidae and Cosmopterigidae nested within it, and Parametriotinae associated with several families previously considered unrelated to them. Using the phylogenetic trees, we examined patterns of life history evolution and determinants of the success of different lineages. Gelechioids express unusually wide variability in life-history strategies, including herbivorous, saprophagous, fungivorous, and carnivorous lineages. Most species are highly specialized in diet and other life history traits. The results suggest that either saprophagy was the ancestral feeding strategy from which herbivory evolved independently on multiple occasions, or that the ancestor was herbivorous with repeated origins of saprophagy. External feeding is an ancestral trait from which internal feeding evolved independently several times. In terms of species number, saprophages are dominant in Australia, while elsewhere several phytophagous lineages have extensively specialized and diversified. Internal feeding has remained a somewhat less generally adopted feeding mode, although in a few lineages significant radiations of leaf mining species have occurred. We conclude that diverse feeding modes, specialization among saprophages, repeated shifts to phytophagy, and a generally high specialization rate on single plant species (monophagy) are the major factors behind the success of the Gelechioidea.     

Phylogeny of the bee genus Agapostemon (Hymenoptera: Halictidae)

Abstract. A phylogeny for genus Agapostemon (Hymenoptera: Halictidae) is reconstructed from morphological characters, using all species, with four representatives of Agapostemonini as outgroup taxa. Parsimony analysis using 150 unordered characters resulted in eighteen equally parsimonious trees, a strict consensus of which is highly resolved for Agapostemon. Based on this analysis, Agapostemonoides Roberts & Brooks is returned to generic status, and a new subgenus is described: Notagapostemon, which includes the rhopalocerus, heterurus, atrocaeruleus, erebus, kohliellus, nasutus and intermedius groups of Moure & Hurd. Species groups are proposed for Notagapostemon and revised in A. (Agapostemon). Agapostemon cockerelli Crawford is synonymized with A. obliquus (Provancher), A. epichryseus (Morelos) with A. leunculus Vachal, A. inca Roberts with A. heterurus Cockerell, A. hispaniolicus Roberts female with A. centratus (Vachal) and A. hispaniolicus Roberts male with A. alayoi Roberts. Optimization of known behaviours suggests communal ancestry for the genus and infers the prevalence of this behaviour in Agapostemon. Optimization of geographical range suggests a Central American or Caribbean origin of Agapostemon, with one invasion of North America and multiple invasions of South America and the Caribbean. One invasion of the Caribbean suggests arrival from North America via Florida.     

Phylogeny of the dragonfly genus Sympetrum (Odonata: Libellulidae)

The libellulid dragonfly genus Sympetrum has been recognized since 1833, but lacks any morphological synapomorphies to unite the taxon. Previous researchers have disagreed over which species belong in Sympetrum, bringing the monophyly of the genus into question. We use DNA sequence data from 6 genetic loci (16S, tRNA-valine, 12S, elongation factor 1 alpha, cytochrome oxidase subunit I, and the second internal transcribed spacer region) and 25 morphological characters (mainly genitalic) to test the monophyly of Sympetrum with Bayesian inference and maximum likelihood analyses. Under Bayesian inference, all Sympetrum species included in this study form a clade, which also contains the Hawaiian monotypic genus Nesogonia, often considered a close relative of Sympetrum. Phylogenetic analyses also reveal at least six strongly supported clades (treated as species groups) within Sympetrum, but relationships between these species groups remain unresolved or unsupported. Although the relationships between Sympetrum species groups remain unresolved, several species groups include taxa from multiple biogeographic regions/continents, and the species group sister to the rest of Sympetrum contains migratory species from the New World and Africa. This pattern suggests a complex biogeographic history in Sympetrum shaped by vicariance and dispersal. Preliminary estimates of the divergence dates of Sympetrum species groups outline a rapid radiation of the groups approximately 32-38 million years ago, possibly influenced by cooling and drying climates of the late Eocene and early Oligocene.     

Origin of the endemic fern genus Diellia coincides with the renewal of Hawaiian terrestrial life in the Miocene

The enigmatic fern genus Diellia, endemic to the Hawaiian archipelago, consists of five extant and one recently extinct species. Diellia is morphologically highly variable, and a unique combination of characters has led to several contrasting hypotheses regarding the relationship of Diellia to other ferns. A phylogenetic analysis of four chloroplast loci places Diellia within 'black-stemmed' rock spleenworts of the species-rich genus Asplenium, as previously suggested by W. H. Wagner. Using an external calibration point, we estimate the divergence of the Diellia lineage from its nearest relatives to have occurred at ca. 24.3 Myr ago matching an independent estimate for the renewal of Hawaiian terrestrial life (ca. 23 Myr ago). We therefore suggest that the ancestor of the Diellia lineage may have been among the first successful colonists of the newly emerging islands in the archipelago. Disparity between morphological and nucleotide sequence variation within Diellia is consistent with a recent rapid radiation. Our estimated time of the Diellia radiation (ca. 2 Myr ago) is younger than the oldest island of Kaua'i (ca. 5.1 Myr ago) but older than the younger major islands of Maui (ca. 1.3 Myr ago), Lana'i (ca. 1.3 Myr ago) and Hawaii (ca. 0.43 Myr ago).     

Phylogeny of the water strider genus Rheumatobates (Heteroptera: Gerridae)

The genus Rheumatobates comprises thirty‐seven species and subspecies of New World water striders belonging to subfamily Rhagadotarsinae. Among species, males vary dramatically in the degree and nature of modifications of the antennae, three pairs of legs and abdominal and genital segments. Characters describing this modification have traditionally been used to differentiate and group species. The general assumption has been that modified species belong to one group and unmodified species to another. These two ‘species groups’ are subdivided into ‘subgroups’, but little effort has been made to resolve relationships among them. We conduct the first numerical cladistic analysis of Rheumatobates using a data set comprised of 102 characters, primarily describing modification of male external morphology. To address concerns about the inclusion of characters to be optimized on the phylogeny, characters describing modification of antennae and hind legs were included and then excluded in separate analyses. A preferred phylogeny was chosen from the four equally parsimonious cladograms found after successive reweighting of characters. There was good resolution at all levels of the phylogeny. Most of the major clades and terminal relationships were moderately to strongly supported, whereas the basal relationships were less well supported. The general assumption that unmodified and modified species form two monophyletic groups was not supported. However, traditionally recognized ‘subgroups’ within the modified species group were largely upheld. The analysis also suggested several major clades and relationships among these clades that were not previously recognized. The exclusion of characters describing modification of antennae and hind legs did not change the resolved major clades of the reconstructed phylogeny.     

Phylogeny of the genus Pythium and description of new genera

Phylogeny of the genus Pythium is analyzed based on sequences of the large subunit ribosomal DNA D1/D2 region and cytochrome oxidase II gene region of Pythium isolates and comprehensive species of related taxa belonging to the Oomycetes. The phylogenetic trees show that the genus Pythium is a highly divergent group and divided into five well- or moderately supported monophyletic clades. Each clade is characterized by sporangial morphology such as globose, ovoid, elongated, or filamentous shapes. Based on phylogeny and morphology, the genus Pythium (s. str.) is emended, and four new genera, Ovatisporangium, Globisporangium, Elongisporangium, and Pilasporangium, are described and segregated from Pythium s. lato.     

Phylogeny and biogeography of the parrot genus Prioniturus (Aves: Psittaciformes)

The parrot genus Prioniturus occurs in the oceanic Philippines, Palawan and Wallacea, a geologically dynamic region with a complex history of land and sea. The described taxa of Prioniturus have been variously placed in different assemblages, and different numbers of species have been recognized. However, a phylogenetic framework is so far lacking. This would be the prerequisite to reconstructing dispersal and colonization patterns of Prioniturus across and within Wallacea and the Philippines. Following our robustly supported phylogenetic hypothesis based on two mitochondrial genes, we propose to treat Prioniturus mindorensis comb. nov. as well as Prioniturus montanus and Prioniturus waterstradti as separate species. In Prioniturus discurus discurus and Prioniturus discurus whiteheadi, further studies using additional data and specimens are necessary to clarify their taxonomic status. This result is congruent with other studies demonstrating that alpha diversity of the Philippine avifauna is strongly underestimated. According to our biogeographic reconstruction, Prioniturus has diversified by a complex combination of colonization of islands and subsequent divergence in allopatry among and within island groups. Dispersal between Sulawesi/Wallacea and the Philippines occurred twice and documents a rare case of faunal exchange between these two regions.     

Phylogeny and systematics of the anamorphic, entomopathogenic genus Beauveria

Beauveria is a cosmopolitan anamorphic genus of arthropod pathogens that includes the agronomically important species, B. bassiana and B. brongniartii, which are used as mycoinsecticides for the biological control of pest insects. Recent phylogenetic evidence demonstrates that Beauveria is monophyletic within the Cordycipitaceae (Hypocreales), and both B. bassiana and B. brongniartii have been linked developmentally and phylogenetically to Cordyceps species. Despite recent interest in the genetic diversity and molecular ecology of Beauveria, particularly as it relates to their role as pathogens of insects in natural and agricultural environments, the genus has not received critical taxonomic review for several decades. A multilocus phylogeny of Beauveria based on partial sequences of RPB1, RPB2, TEF and the nuclear intergenic region, Bloc, is presented and used to assess diversity within the genus and to evaluate species concepts and their taxonomic status. B. bassiana and B. brongniartii, both which represent species complexes and which heretofore have lacked type specimens, are redescribed and types are proposed. In addition six new species are described including B. varroae and B. kipukae, which form a biphyletic, morphologically cryptic sister lineage to B. bassiana, B. pseudobassiana, which also is morphologically similar to but phylogenetically distant from B. bassiana, B. asiatica and B. australis, which are sister lineages to B. brongniartii, and B. sungii, an Asian species that is linked to an undetermined species of Cordyceps. The combination B. amorpha is validly published and an epitype is designated.     

Phylogeny of the genus Omphalotus based on nuclear ribosomal DNA-sequences

The evolutionary history of the genus Omphalotus was inferred from DNA sequences of the ITS1-5.8S-ITS2 rDNA region. We analyzed 32 collections from different geographical areas: O. olearius (Europe), O. illudens (Europe, North America), O. subilludens (North America), O. olivascens var. olivascens (North America) and var. indigo (Mexico), O. mexicanus (Middle America), O. nidiformis (Australia), and O. japonicus (Japan). Phylogenetic analysis was performed declaring Nothopanus eugrammus as outgroup. Our analyses show that the genus Omphalotus is split into two major clades, the first consisting of O. illudens and O. mexicanus and the second comprising O. olearius, O. olivascens, O. japonicus, O. nidiformis and O. subilludens. Moreover, the often discussed synonymy of O. illudens and O. olearius is rejected. Omphalotus japonicus, a species formerly placed in the genus Lampteromyces Sing. for morphological reasons, clustered as the sister group of O. olearius.     

Phylogeny and taxonomy of the genus Phylloporia (Hymenochaetales)

Based on 28 taxa, including six species of Phylloporia, and respectively one representative of 17 genera of the Hymenochaetales, a phylogenetic analysis of a region of the large subunit of the nuclear encoded ribosomal DNA was performed. Molecular sequence data as well as morphological and anatomical features show the genus to be monophyletic. Next related to Phylloporia is Fulvifomes. The phylogenetic relationships of Phylloporia are discussed. In addition the genus Phylloporia is monographed; 12 species are accepted and described with a key.     

Phylogeny for the faint of heart: a tutorial

Phylogenetic trees seem to be finding ever broader applications, and researchers from very different backgrounds are becoming interested in what they might have to say. This tutorial aims to introduce the basics of building and interpreting phylogenetic trees. It is intended for those wanting to understand better what they are looking at when they look at someone else's trees or to begin learning how to build their own. Topics covered include: how to read a tree, assembling a dataset, multiple sequence alignment (how it works and when it does not), phylogenetic methods, bootstrap analysis and long-branch artefacts, and software and resources.     

Phylogeny and habitat adaptations within a monophyletic group of wetland moss genera (Amblystegiaceae)

Genus level phylogenetic patterns within a monophyletic group of wetland mosses consisting ofTomentypnum, Hamatocaulis, Scorpidium, Conardia, Calliergon, Warnstorfia, Straminergon, andLoeskypnum (Amblystegiaceae) are cladistically analysed, usingPalustriella and partlyCratoneuron as outgroups. The ingroup consists of two clades, one withTomentypnum, Hamatocaulis andScorpidium, the other with the other ingroup genera. The second clade gets completely resolved only with the inclusion of habitat data. The adaptation to relatively dry wetland habitats probably evolved in the ancestor ofStraminergon andLoeskypnum, the species ofCalliergon andWarnstorfia, which are more ancestral, growing in wetter habitats. The more primitive taxa of the ingroup, as well asPalustriella species, occur in relatively mineral-rich habitats and adaptations to poorer habitats occurred several times in the two clades.