Major Lineages (major + lineage)

Distribution by Scientific Domains
Distribution within Life Sciences

Selected Abstracts


Hwan Su Yoon
Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well-supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1,3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter-clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella, and Erythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, and Rufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera). [source]

In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth

Trine Rolighed Thomsen
Summary Among the filamentous bacteria occasionally causing bulking problems in activated sludge treatment plants, three morphotypes with attached microbial growth are common, Eikelboom Type 0041, Type 1851 and Type 1701. A better knowledge of the phylogeny and physiology of these filamentous bacteria is necessary in order to develop control strategies for bulking. In this study we have used a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR) to investigate the identity and in situ physiology of the Type 0041-morphotype and its attached bacteria in two wastewater treatment plants. Identification and enumeration of Type 0041 using group-specific 16S rRNA-targeted FISH probes revealed that approximately 15% of the filaments hybridized with a gene probe specific for the TM7 group, a recently recognized major lineage in the bacterial domain. All other filaments morphologically identified as Type 0041 only hybridized to the general bacterial EUB338-probe, indicating that they probably do not belong to commonly isolated bacterial phyla such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, for which group-specific probes were used. The phylogenetic heterogeneity of Type 0041 again highlights the inadequacy of a morphology-based classification system. Like the filaments, most of the attached microbial cells were not identified beyond their affiliation to the Bacteria using the group-specific FISH probes. However, several different bacterial phyla were represented in the identified fraction suggesting that the attached microorganisms are phylogenetically diverse. The study of the in situ physiology of Type 0041 using MAR-FISH revealed that both the filaments and the attached bacteria on Type 0041 were versatile in the use of organic substrates and electron acceptors. It was observed that all Type 0041 could consume glucose, but none of the filaments were able to consume acetate under any conditions tested, in contrast to some of the attached bacteria. No significant physiological differences were found between TM7,positive and TM7,negative Type 0041 filaments, and only minor differences were observed between the two treatment plants tested. These are the first data on the physiology of the almost entirely uncharacterized TM7 phylum and show that TM7 filamentous bacteria can uptake carbon substrates under aerobic and anaerobic conditions. [source]

Phylogeny and ecological radiation of New World thistles (Cirsium, Cardueae , Compositae) based on ITS and ETS rDNA sequence data

Dean G. Kelch
Abstract Sequence data from a portion of the external transcribed spacer (ETS) and internal transcribed spacers (ITS-1 and ITS-2) of 18S-26S nuclear ribosomal DNA were used to resolve historical biogeography and ecology of true thistles (Cirsium, Cardueae, Compositae) in the New World. The 650 base-pair, 3, portion of the ETS examined here showed a level of variation across taxa similar to that of the ITS sequences included. A maximum-likelihood tree based on combined ETS and ITS sequences leads us to suggest that the New World species of true thistles constitute a major lineage, which in turn comprises several smaller lineages. A western North American lineage shows weak quartet-puzzling support, but includes a well-supported lineage of species endemic to the California Floristic Province. Comparisons of this Californian lineage with other neoendemic angiosperm groups of the region show that the Californian Cirsium lineage exhibits unusually high ecological diversity for a group displaying such low levels of rDNA sequence divergence across taxa. Similarly low levels of sequence divergence were found throughout the New World Cirsium lineage. These results indicate either that Cirsium underwent a rapid ecological radiation in North America, or that rDNA evolution in North American Cirsium has been highly conservative. [source]

Reproductive hierarchies in the African allodapine bee Allodapula dichroa (Apidae: Xylocopinae) and ancestral forms of sociality

The social organization of allodapine bees has been described in detail for most genera, although there remains a notable gap for one major lineage, the genus Allodapula. Here, we provide the first detailed study of social organization in Allodapula dichroa. Colony sizes are small and the frequency of cooperative nesting is low compared with other allodapine taxa, but there is very clear evidence for reproductive differentiation among adult nestmates. Reproductively dominant females tend to be larger than their nestmates and have much higher levels of wing wear, suggesting that they perform most foraging activities. Multi-female colonies have: (1) lower rates of complete brood absence, suggesting a substantial benefit to cooperative nesting; and (2) larger numbers of brood, suggesting that the presence of a second adult female leads to a greater reproductive output. These data suggest a major phylogenetic split in the form of social organization within the allodapines. In the genus Macrogalea (sister clade to all other allodapines), body size does not preclude young females from laying eggs, and there appears to be, at most, weak reproductive queues. However, in most other allodapines, reproductive hierarchies are prominent and younger and/or smaller females queue for reproductive opportunities, adopt permanently subordinate roles, or disperse. Interestingly, the most common forms of reproductive hierarchies in allodapines do not involve subordinates undertaking foraging roles before reproduction, but instead involve the delaying of both reproduction and foraging. This has implications for the understanding of suggested developmental ground plans in the early stages of social evolution. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 520,530. [source]

Four- and five-color flow cytometry analysis of leukocyte differentiation pathways in normal bone marrow: A reference document based on a systematic approach by the GTLLF and GEIL,,

CYTOMETRY, Issue 1 2010
Christine Arnoulet
Abstract Background: The development of multiparameter flow cytometry (FCM) and increasingly sophisticated analysis software has considerably improved the exploration of hematological disorders. These tools have been widely applied in leukaemias, lymphomas, and myelodysplasias, yet with very heterogeneous approaches. Consequently, there is no extensive reference document reporting on the characteristics of normal human bone marrow (BM) in multiparameter FCM. Here, we report a reference analysis procedure using relevant antibody combinations in normal human BM. Methods: A first panel of 23 antibodies, constructed after literature review, was tested in four-color combinations (including CD45 in each) on 30 samples of BM. After evaluation of the data, a second set of 22 antibodies was further applied to another 35 BM samples. All list-modes from the 65 bone marrow samples were reviewed collectively. A systematised protocol for data analysis was established including biparametric representations and color codes for the three major lineages and undifferentiated cells. Results: This strategy has allowed to obtain a reference atlas of relevant patterns of differentiation antigens expression in normal human BM that is available within the European LeukemiaNet. This manuscript describes how this atlas was constructed. Conclusions: Both the strategy and atlas could prove very useful as a reference of normality, for the determination of leukemia-associated immunophenotypic patterns, analysis of myelodysplasia and, ultimately, investigation of minimal residual disease in the BM. © 2009 Clinical Cytometry Society [source]

Comparative morphology and evolutionary pathways of the mouthparts in spore-feeding Staphylinoidea (Coleoptera)

ACTA ZOOLOGICA, Issue 3 2003
Oliver Betz
Abstract This study surveys the external morphology of the mouthparts in the guild of spore-feeders among the coleopterous superfamily Staphylinoidea, evaluating the influence of different phylogenetic and ecological starting points on the formation of their mouthparts. Our emphasis is on a scanning electron microscope analysis (SEM) of the involved trophic structures in spore-feeding larvae and adults of the Ptiliidae, Leiodidae and Staphylinidae, describing the fine structure of their main functional elements. Functionally, mouthpart structures resemble brushes, brooms, combs, rakes, rasps, excavators, knives, thorns, cram-brushes, bristle troughs, blocks and differently structured grinding surfaces. Their different involvement in the various aspects of the feeding process (i.e. food gathering, transporting, channelling and grinding) is deduced from our SEM analyses plus direct video observations. We infer five different patterns of food transport and processing, discriminating adults of ptiliids, leiodids plus staphylinids (excluding some aleocharines), several aleocharine staphylinids, and the larvae of leiodids and staphylinids. The structural diversity of the mouthparts increases in the order from (1) Ptiliidae, (2) Leiodidae towards (3) Staphylinidae, reflecting the increasing systematic and ecological diversity of these groups. Comparisons with non-spore-feeders show that among major lineages of staphylinoids, shifts from general microphagy to sporophagy are not necessarily constrained by, nor strongly reflected in, mouthpart morphology. Nevertheless, in several of these lineages the organs of food intake and grinding have experienced particular fine-structural modifications, which have undergone convergent evolution, probably in response to specialized mycophagy such as spore-feeding. These modifications involve advanced galeal rakes, galeal or lacinial ,spore brushes' with arrays of stout bristles, reinforced obliquely ventrad orientated prosthecal lobes and the differentiations of the molar grinding surfaces into stout teeth or tubercles. In addition, several staphylinids of the tachyporine and oxyteline groups with reduced mandibular molae have evolved secondary trituration surfaces, which in some aleocharines are paralleled by considerable re-constructions of the labium,hypopharynx. [source]

Host specificity of ambrosia and bark beetles (Col., Curculionidae: Scolytinae and Platypodinae) in a New Guinea rainforest

Abstract 1.,Bark and ambrosia beetles are crucial for woody biomass decomposition in tropical forests worldwide. Despite that, quantitative data on their host specificity are scarce. 2.,Bark and ambrosia beetles (Scolytinae and Platypodinae) were reared from 13 species of tropical trees representing 11 families from all major lineages of dicotyledonous plants. Standardised samples of beetle-infested twigs, branches, trunks, and roots were taken from three individuals of each tree species growing in a lowland tropical rainforest in Papua New Guinea. 3.,A total of 81 742 beetles from 74 species were reared, 67 of them identified. Local species richness of bark and ambrosia beetles was estimated at 80,92 species. 4.,Ambrosia beetles were broad generalists as 95% of species did not show any preference for a particular host species or clade. Similarity of ambrosia beetle communities from different tree species was not correlated with phylogenetic distances between tree species. Similarity of ambrosia beetle communities from individual conspecific trees was not higher than that from heterospecific trees and different parts of the trees hosted similar ambrosia beetle communities, as only a few species preferred particular tree parts. 5.,In contrast, phloeophagous bark beetles showed strict specificity to host plant genus or family. However, this guild was poor in species (12 species) and restricted to only three plant families (Moraceae, Myristicaceae, Sapindaceae). 6.,Local diversity of both bark and ambrosia beetles is not driven by the local diversity of trees in tropical forests, since ambrosia beetles display no host specificity and bark beetles are species poor and restricted to a few plant families. [source]

Insight into diversity, body size and morphological evolution from the largest Early Cretaceous enantiornithine bird

Zhonghe Zhou
Abstract Most of Mesozoic bird diversity comprises species that are part of one of two major lineages, namely Ornithurae, including living birds, and Enantiornithes, a major radiation traditionally referred to as ,opposite birds'. Here we report the largest Early Cretaceous enantiornithine bird from north-east China, which provides evidence that basal members of Enantiornithes share more morphologies with ornithurine birds than previously recognized. Morphological evolution in these two groups has been thought to be largely parallel, with derived members of Enantiornithes convergent on the ,advanced' flight capabilities of ornithurine birds. The presence of an array of morphologies previously thought to be derived within ornithurine and enantiornithine birds in a basal enantiornithine species provides evidence of the complex character evolution in these two major lineages. The cranial morphology of the new specimen is among the best preserved for Mesozoic avians. The new species extends the size range known for Early Cretaceous Enantiornithes significantly and provides evidence of forelimb to hind limb proportions distinct from all other known members of the clade. As such, it sheds new light on avian body size evolution and diversity, and allows a re-evaluation of a previously proposed hypothesis of competitive exclusion among Early Cretaceous avian clades. [source]

Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data

Martin Irestedt
Phylogenetic relationships among major groups of passeriform birds were studied by analyses of nucleotide sequence data from two nuclear genes, c- myc and RAG-1. The results corroborated both the monophyly of the order Passeriformes, and the major dichotomy into oscine and suboscine passerines previously suggested based on syringeal morphology and DNA-DNA hybridizations. The representatives of the Old World suboscines (families Eurylaimidae, Philepittidae and Pittidae) formed a monophyletic clade. The New World suboscines clustered into two clades. The first contained Conopophaga (Conopophagidae), Furnarius (Furnariidae), Lepidocolaptes (Dendrocolaptidae), Thamnophilus (Formicariidae), and Rhinocrypta (Rhinocryptidae). Previously, the monophyly of this group has been inferred from their possession of a unique, "tracheophone" syrinx, and from DNA-DNA hybridisation data. The second clade of New World suboscines includes Gubernetes and Muscivora (Tyrannidae), Phytotoma (Phytotomidae), Tityra (Cotingidae) and Pipra (Pipridae). This group of families have been considered monophyletic based on morphology (although ambiguously) and DNA-DNA hybridisation. The sister group relationship of Tityra and Phytotoma supports the previously supposed cotingid affinity of Phytotoma. Nuclear DNA data also unambiguously group the lyrebirds Menura with the oscines. The presented results from the analysis of nuclear DNA agree well with morphology and DNA-DNA hybridisation data. The precise age of the divergences studied herein are unknown but based on interpretations of the fossil record of passerine birds many of them might date back to the early Tertiary. The agreement between data from the nuclear DNA and other sources, along with the fact that neither of the studied genes showed sign of saturation, indicate the great potential of these two nuclear genes to resolve very old divergences in birds. [source]

Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in Thailand

Pattanop Kanokratana
The prokaryotic diversity in the Bor Khlueng hot spring in Ratchaburi province, Thailand was investigated by a culture-independent molecular approach. This hydrothermal pool is located in the central part of Thailand and contains sulfide-rich mineral water that is believed to relieve muscle ache and pain. The water flow year-round with temperature ranging between 50,57 °C. Community DNA was extracted directly from sediment samples by coring to depth of ,20,30 cm. Small-subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific for the domains Archaea and Bacteria. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 200 clones were randomly selected for further analyses. After restriction fragment length polymorphism (RFLP) analysis of rDNA clones and exclusion of chimeric sequences 36 phylotypes were obtained. The Bor Khlueng phylotypes spanned a wide range within the domain Bacteria, occupying eleven major lineages (phyla). Almost a quarter (23%) of the clones were classifed as Acidobacteria. The other clones were grouped into the Bacteriodetes (19%), Nitrospirae (13%), Proteobacteria (12%), Deinococcus-Thermus lineage (11%), planctomycetes (6%), and Verrucomicrobia (5%). The four remaining phyla, 5% each, were assigned to Actinobacteria, Chloroflexi, Cyanobacteria, and the candidate division "OP10". For the archaeal 16S rRNA gene sequence library, 25 distinct phylotypes were obtained, 17 clones were found to be associated with Crenarahaeota and 8 clones were associated with Euryarachaeota. The findings of the molecular survey of this so far not investigated site showed that Bor Khlueng hot spring is a potential rich source of unique bacterial and archaeal species. The great majority (,80%) of the prokaryotic sequences detected in Bor Khlueng were unknown. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Phylogeographic structuring and volant mammals: the case of the pallid bat (Antrozous pallidus)

Sarah E. Weyandt
Abstract Aim, To examine the phylogeographic pattern of a volant mammal at the continental scale. The pallid bat (Antrozous pallidus) was chosen because it ranges across a zone of well-studied biotic assemblages, namely the warm deserts of North America. Location, The western half of North America, with sites in Mexico, the United States, and Canada. Methods, PCR amplification and sequencing of the mitochondrial control region was performed on 194 pallid bats from 36 localities. Additional sequences at the cytochrome- b locus were generated for representatives of each control-region haplotype. modeltest was used to determine the best set of parameters to describe each data set, which were incorporated into analyses using paup*. Statistical parsimony and measurements of population differentiation (amova, FST) were also used to examine patterns of genetic diversity in pallid bats. Results, We detected three major lineages in the mitochondrial DNA of pallid bats collected across the species range. These three major clades have completely non-overlapping geographic ranges. Only 6 of 80 control-region haplotypes were found at more than a single locality, and sequences at the more conserved cytochrome- b locus revealed 37 haplotypes. Statistical parsimony generated three unlinked networks that correspond exactly to clades defined by the distance-based analysis. On average there was c. 2% divergence for the combined mitochondrial sequences within each of the three major clades and c. 7% divergence between each pair of clades. Molecular clocks date divergence between the major clades at more than one million years, on average, using the faster rates, and at more than three million years using more conservative rates of evolution. Main conclusions, Divergent haplotypic lineages with allopatric distributions suggest that the pallid bat has responded to evolutionary pressures in a manner consistent with other taxa of the American southwest. These results extend the conclusions of earlier studies that found the genetic structuring of populations of some bat species to show that a widespread volant species may comprise a set of geographically replacing monophyletic lineages. Haplotypes were usually restricted to single localities, and the clade showing geographic affinities to the Sonoran Desert contained greater diversity than did clades to the east and west. While faster molecular clocks would allow for glacial cycles of the Pleistocene as plausible agents of diversification of pallid bats, evidence from co-distributed taxa suggests support for older events being responsible for the initial divergence among clades. [source]

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

L. Zhang
The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8·89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4·78 mya from the Chinese group. The northern,southern clades of S. nigripinnis began to diverge c. 2·12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0·34 mya. [source]

Comparative morphology of the hemolymph vascular system in scorpions,A survey using corrosion casting, MicroCT, and 3D-reconstruction

Christian S. Wirkner
Abstract Although scorpions are one of the better known groups of Arthropoda, detailed knowledge of their anatomy remains superficial. This contribution presents the first comprehensive investigation of the gross morphology of the scorpion vascular system, based on a survey of species representing all major lineages of the order, using classical and modern non-destructive techniques in combination with three-dimensional reconstruction. The investigation reveals that the hemolymph vascular system (HVS) of Scorpiones comprises a central pumping heart which extends the entire length of the mesosoma and is enclosed in a pericardium. Several arteries branch off the heart to supply different organs and body regions. Two different anterior aorta major branching patterns are identified among the species investigated. Arteries that branch off the anterior aorta system supply the appendages (chelicerae, pedipalps, and walking legs) and the central nerve mass with a complex arterial network. This study of the HVS of scorpions provides further evidence that the vascular systems of euarthropods can be highly complex. Use of the term "open circulatory system" within arthropods is re-emphasized, as it refers to the general organization of the body cavity (i.e. mixocoely) rather than to the complexity of the circulatory system. J. Morphol., 2007. © 2007 Wiley-Liss, Inc. [source]


Galice Hoarau
Eukaryotic mitochondria are mostly uniparentally (maternally) inherited, although mtDNA heteroplasmy has been reported in all major lineages. Heteroplasmy, the presence of more than one mitochondrial genome in an individual, can arise from recombination, point mutations, or by occasional transmission of the paternal mtDNA (=paternal leakage). Here, we report the first evidence of mtDNA paternal leakage in brown algae. In Denmark, where Fucus serratus L. and Fucus evanescens C. Agardh have hybridized for years, we found eight introgressed individuals that possessed the very distinct haplotypes of each parental species. The finding of heteroplasmy in individuals resulting from several generations of backcrosses suggests that paternal leakage occurred in earlier generations and has persisted through several meiotic bottlenecks. [source]


Hwan Su Yoon
Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well-supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1,3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter-clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella, and Erythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, and Rufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera). [source]

A phylogeny of anisopterous dragonflies (Insecta, Odonata) using mtRNA genes and mixed nucleotide/doublet models

G. Fleck
Abstract The application of mixed nucleotide/doublet substitution models has recently received attention in RNA-based phylogenetics. Within a Bayesian approach, it was shown that mixed models outperformed analyses relying on simple nucleotide models. We analysed an mt RNA data set of dragonflies representing all major lineages of Anisoptera plus outgroups, using a mixed model in a Bayesian and parsimony (MP) approach. We used a published mt 16S rRNA secondary consensus structure model and inferred consensus models for the mt 12S rRNA and tRNA valine. Secondary structure information was used to set data partitions for paired and unpaired sites on which doublet or nucleotide models were applied, respectively. Several different doublet models are currently available of which we chose the most appropriate one by a Bayes factor test. The MP reconstructions relied on recoded data for paired sites in order to account for character covariance and an application of the ratchet strategy to find most parsimonious trees. Bayesian and parsimony reconstructions are partly differently resolved, indicating sensitivity of the reconstructions to model specification. Our analyses depict a tree in which the damselfly family Lestidae is sister group to a monophyletic clade Epiophlebia + Anisoptera, contradicting recent morphological and molecular work. In Bayesian analyses, we found a deep split between Libelluloidea and a clade ,Aeshnoidea' within Anisoptera largely congruent with Tillyard's early ideas of anisopteran evolution, which had been based on evidently plesiomorphic character states. However, parsimony analysis did not support a clade ,Aeshnoidea', but instead, placed Gomphidae as sister taxon to Libelluloidea. Monophyly of Libelluloidea is only modestly supported, and many inter-family relationships within Libelluloidea do not receive substantial support in Bayesian and parsimony analyses. We checked whether high Bayesian node support was inflated owing to either: (i) wrong secondary consensus structures; (ii) under-sampling of the MCMC process, thereby missing other local maxima; or (iii) unrealistic prior assumptions on topologies or branch lengths. We found that different consensus structure models exert strong influence on the reconstruction, which demonstrates the importance of taxon-specific realistic secondary structure models in RNA phylogenetics. [source]

Differentiation of golden-ringed dragonfly Anotogaster sieboldii (Selys, 1854) (Cordulegastridae: Odonata) in the insular East Asia revealed by the mitochondrial gene genealogy with taxonomic implications

T. Kiyoshi
Abstract Molecular phylogeographical analyses of Anotogaster sieboldii (Selys, 1854) were conducted to reveal the differentiation process of insular populations. The gene genealogy based on 845 bp of the mitochondrial genes (cytochrome oxidase subunit I and subunit II) indicated that A. sieboldii includes two deeply separated lineages. These two major lineages seem to have differentiated in Miocene before the formation of the insular East Asia. One lineage includes three inner clades that correspond to the populations of northern area (the Japanese main islands, Korean Peninsula, Yakushima), Amamioshima and Okinawajima. Populations of Central Ryukyu, including Amamioshima and Okinawajima, might have been divided from the northern populations in early Pleistocene. The other major lineage includes populations of the Yaeyama Group, Taiwan and East China. The former two populations were reconstructed as a reciprocal monophyletic group. Populations of Taiwan and Yaeyama Groups would have been separated from the continental ones in Pleistocene. These two highly divergent lineages should be recognized as distinct species. Furthermore, the mitochondrial lineages revealed six genetically distinct and geographically isolated assemblages: (1) northern populations, (2) Amamioshima, (3) Okinawajima, (4) Yaeyama Group, (5) Taiwan and (6) East China. Zusammenfassung An der Libelle Anotogaster sieboldii wurden molekulare phylogeographische Analysen durchgeführt, um ihre Differenzierungen in Insel-Populationen zu erkennen. Die Gen-Genealogie (basierend auf 845 bp mitochondrialer Gene (COI und COII) zeigte, dass A. sieboldii zwei weit getrennte Abstammungslinien enthält, die sich wahrscheinlich im Miozän vor der Bildung der ostasiatischen Inselwelt differenzierten. Eine Abstammungslinie schließt drei Gruppierungen ein, die den Populationen in den nördlichen Gebieten entsprechen: die japanischen Hauptinseln, die koreanische Halbinsel Yakushima, Amamioshima sowie Okinawajima. Die Populationen von Zentral-Ryukyu, einschließlich Amamioshima und Okinawajima, ist möglicherweise im frühen Pleistozän von den nördlichen Populationen getrennt worden. Die andere größere Abstammungslinie schließt die Populationen der Yaeyama-Gruppe, Taiwan und das Östliche China ein. Zwei dieser Populationen wurden als Teil einer entsprechenden monophyletischen Gruppe rekonstruiert; die Populationen von Taiwan und die Yaeyama-Gruppe sind danach im Pleistozän von den kontinentalen Populationen getrennt worden. Diese zwei sehr differierenden Abstammungslinien sollten als verschiedene Spezies betrachtet werden. Weiterhin werden sechs genetisch verschiedene und geographisch isolierte Gruppierungen deutlich: (1) die nördlichen Populationen, (2) Amamioshima, (3) Okinawajima, (4) die Yaeyama-Gruppe, (5) Taiwan und (6) die Population im östlichen China. [source]

The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR)

J. Hess
Abstract Phylogenetic relationships in the Olea europaea complex and the phylogeography of 24 populations of the Macaronesian olive (O. europaea ssp. cerasiformis) were assessed by using three molecular markers: nuclear ribosomal internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Parsimony analysis of the ITS-1 sequences and Neighbour-joining (NJ) analyses of RAPD and ISSR banding variation revealed four major lineages in the O. europaea complex: (1) ssp. cuspidata; (2) ssp. cerasiformis from Madeira; (3) ssp. laperrinei; and (4) ssp. cerasiformis from the Canary Islands plus ssp. europaea. These results provide unequivocal support for two independent dispersal events of Olea to the Madeira and Canary Islands. Molecular and morphological evidence led to recognition of two separate olive taxa in Macaronesia, to date included in ssp. cerasiformis. NJ analyses of the combined RAPD and ISSR data suggest that the colonization of the Canaries by O. europaea may have followed an east to west stepping-stone model. An interisland dispersal sequence can be recognized, starting from the continent to Fuerteventura, Gran Canaria, Tenerife, La Gomera, and finally La Palma. High dispersal activity of the lipid-rich Olea fruits by birds in the Mediterranean region is congruent with multiple dispersal of olives to Macaronesia and successive colonization of the archipelagos. The observation of strong genetic isolation between populations of different islands of the Canary Islands suggests, however, that subsequent interisland dispersal and establishment has been very rare or may not have occurred at all. [source]


Abstract:,Eshanosaurus deguchiianus is based on a single left dentary from the Lower Lufeng Formation (Lower Jurassic) of Yunnan Province, China. It was originally identified as the earliest known member of Therizinosauroidea (Theropoda: Coelurosauria), a conclusion that results in a significant downward range extension for this clade (>65 million years) and for many other major lineages within Coelurosauria. However, this interpretation has been questioned and several authors have proposed that the anatomical features used to refer Eshanosaurus to Therizinosauroidea are more consistent with attribution to a basal sauropodomorph dinosaur. Detailed consideration of the holotype specimen suggests that several features of the dentary and dentition exclude Eshanosaurus from Sauropodomorpha and support its inclusion within Therizinosauroidea. If accepted as an Early Jurassic coelurosaur, Eshanosaurus has important implications for understanding the timing and tempo of early theropod diversification. Moreover, its provenance also suggests that substantial portions of the coelurosaur fossil record may be missing or unsampled. However, the Early Jurassic age of Eshanosaurus requires confirmation if this taxon is to be fully incorporated into broader evolutionary studies. [source]

The Arabidopsis ClpB/Hsp100 family of proteins: chaperones for stress and chloroplast development

Ung Lee
Summary The Casein lytic proteinase/heat shock protein 100 (Clp/Hsp100) proteins are chaperones that act to remodel/disassemble protein complexes and/or aggregates using the energy of ATP. In plants, one of the best-studied proteins from this family is cytosolic ClpB1 (At1g74310), better known in Arabidopsis as AtHsp101, which is a heat shock protein required for acclimation to high temperatures. Three other ClpB homologues have been identified in the Arabidopsis genome (ClpB2, ClpB3 and ClpB4; At4g14670, At5g15450 and At2g25140). To define further the roles of these chaperones in plants we investigated their intracellular localization, evolutionary relationships, patterns of expression and the phenotypes of corresponding T-DNA insertion mutants. We first found that ClpB2 was misannotated; there is no functional ClpB/Hsp100 gene at this locus. By fusing the putative transit peptides of ClpB3 and ClpB4 with GFP, we showed that these proteins are targeted to the chloroplast and mitochondrion, respectively, and we therefore designated them as ClpB-p and ClpB-m. Phylogenetic analysis supports two major lineages of ClpB proteins in plants, an ,eukaryotic', cytosol/nuclear-localized group containing AtHsp101, and an organelle-localized lineage, containing both ClpB-p and ClpB-m. Although AtHsp101, ClpB-p and ClpB-m transcripts all accumulate dramatically at high temperatures, the T-DNA insertion mutants of ClpB-p and ClpB-m show no evidence of seedling heat stress phenotypes similar to those observed in AtHsp101 mutants. Strikingly, ClpB-p knockouts were seedling lethals, failing to accumulate chlorophyll or properly develop chloroplasts. Thus, in plants, the function of ClpB/Hsp100 proteins is not restricted to heat stress, but a specific member of the family provides housekeeping functions that are essential to chloroplast development. [source]

Transit peptide diversity and divergence: A global analysis of plastid targeting signals

BIOESSAYS, Issue 10 2007
Nicola J. Patron
Proteins are targeted to plastids by N-terminal transit peptides, which are recognized by protein import complexes in the organelle membranes. Historically, transit peptide properties have been defined from vascular plant sequences, but recent large-scale genome sequencing from the many plastid-containing lineages across the tree of life has provided a much broader representation of targeted proteins. This includes the three lineages containing primary plastids (plants and green algae, rhodophytes and glaucophytes) and also the seven major lineages that contain secondary plastids, "secondhand" plastids derived through eukaryotic endosymbiosis. Despite this extensive spread of plastids throughout Eukaryota, an N-terminal transit peptide has been maintained as an essential plastid-targeting motif. This article provides the first global comparison of transit peptide composition and summarizes conservation of some features, the loss of an ancestral motif from the green lineages including plants, and modifications to transit peptides that have occurred in secondary and even tertiary plastids. BioEssays 29:1048,1058, 2007. © 2007 Wiley Periodicals, Inc. [source]

,After Africa': the evolutionary history and systematics of the genus Charaxes Ochsenheimer (Lepidoptera: Nymphalidae) in the Indo-Pacific region

The predominantly Afrotropical genus Charaxes is represented by 31 known species outside of Africa (excluding subgenus Polyura Billberg). We explored the biogeographic history of the genus using every known non-African species, with several African species as outgroup taxa. A phylogenetic hypothesis is proposed, based on molecular characters of the mitochondrial genes cytochrome oxidase subunit I (COI) and NADH dehydrogenase 5 (ND5), and the nuclear wingless gene. Phylogenetic analyses based on maximum parsimony and Bayesian inference of the combined dataset implies that the Indo-Pacific Charaxes form a monophyletic assemblage, with the exception of Charaxes solon Fabricius. Eight major lineages are recognized in the Indo-Pacific, here designated the solon (+African), elwesi, harmodius, amycus, mars, eurialus, latona, nitebis, and bernardus clades. Species group relationships are concordant with morphology and, based on the phylogeny, we present the first systematic appraisal and classification of all non-African species. A biogeographical analysis reveals that, after the genus originated in Africa, the evolutionary history of Charaxes in the Indo-Pacific, in particular Wallacea, may be correlated with the inferred geological and climatic history of the region. We propose that Wallacea was the area of origin of all Charaxes (excluding C. solon) occurring to the east of Wallace's [1863] Line. The earliest Indo-Pacific lineages appear to have diverged subsequent to the initial fragmentation of a palaeo-continent approximately 13 million years ago. Further diversification in Indo-Pacific Charaxes appears primarily related to climatic changes during the Pliocene and possibly as recently as the Pleistocene. Although both dispersal and vicariance have played important roles in the evolution of the genus within the region, the latter has been particularly responsible for diversification of Charaxes in Wallacea. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 457,481. [source]

Snake phylogeny based on osteology, soft anatomy and ecology

ABSTRACT Relationships between the major lineages of snakes are assessed based on a phylogenetic analysis of the most extensive phenotypic data set to date (212 osteological, 48 soft anatomical, and three ecological characters). The marine, limbed Cretaceous snakes Pachyrhachis and Haasiophis emerge as the most primitive snakes: characters proposed to unite them with advanced snakes (macrostomatans) are based on unlikely interpretations of contentious elements or are highly variable within snakes. Other basal snakes include madtsoiids and Dinilysia, both large, presumably non-burrowing forms. The inferred relationships within extant snakes are broadly similar to currently accepted views, with scolecophidians (blindsnakes) being the most basal living forms, followed by anilioids (pipesnakes), booids and booid-like groups, acrochordids (filesnakes), and finally colubroids. Important new conclusions include strong support for the monophyly of large constricting snakes (erycines, boines, pythonines), and moderate support for the non-monophyly of the ,trophidophiids' (dwarf boas). These phylogenetic results are obtained whether varanoid lizards, or amphisbaenians and dibamids, are assumed to be the nearest relatives (outgroups) of snakes, and whether multistate characters are treated as ordered or unordered. Identification of large marine forms, and large surface-active terrestrial forms, as the most primitive snakes contradicts with the widespread view that snakes arose via minute, burrowing ancestors. Furthermore, these basal fossil snakes all have long flexible jaw elements adapted for ingesting large prey (,macrostomy'), suggesting that large gape was primitive for snakes and secondarily reduced in the most basal living foms (scolecophidians and anilioids) in connection with burrowing. This challenges the widespread view that snake evolution has involved progressive, directional elaboration of the jaw apparatus to feed on larger prey. [source]

Multilocus ribosomal RNA phylogeny of the leaf beetles (Chrysomelidae)

CLADISTICS, Issue 1 2008
Jesús Gómez-Zurita
Basal relationships in the Chrysomelidae (leaf beetles) were investigated using two nuclear (small and partial large subunits) and mitochondrial (partial large subunit) rRNA (, 3000 bp total) for 167 taxa covering most major lineages and relevant outgroups. Separate and combined data analyses were performed under parsimony and model-based tree building algorithms from dynamic (direct optimization) and static (Clustal and BLAST) sequence alignments. The performance of methods differed widely and recovery of well established nodes was erratic, in particular when using single gene partitions, but showed a slight advantage for Bayesian inferences and one of the fast likelihood algorithms (PHYML) over others. Direct optimization greatly gained from simultaneous analysis and provided a valuable hypothesis of chrysomelid relationships. The BLAST-based alignment, which removes poorly aligned sequence segments, in combination with likelihood and Bayesian analyses, resulted in highly defensible trees obtained in much shorter time than direct optimization, and hence is a viable alternative when data sets grow. The main taxonomic findings include the recognition of three major lineages of Chrysomelidae, including a basal "sagrine" clade (Criocerinae, Donaciinae, Bruchinae), which was sister to the "eumolpine" (Spilopyrinae, Eumolpinae, Cryptocephalinae, Cassidinae) plus "chrysomeline" (Chrysomelinae, Galerucinae) clades. The analyses support a broad definition of subfamilies (i.e., merging previously separated subfamilies) in the case of Cassidinae (cassidines + hispines) and Cryptocephalinae (chlamisines + cryptocephalines + clytrines), whereas two subfamilies, Chrysomelinae and Eumolpinae, were paraphyletic. The surprising separation of monocot feeding Cassidinae (associated with the eumolpine clade) from the other major monocot feeding groups in the sagrine clade was well supported. The study highlights the need for thorough taxon sampling, and reveals that morphological data affected by convergence had a great impact when combined with molecular data in previous phylogenetic analyses of Chrysomelidae. © The Willi Hennig Society 2007. [source]

Systematics and Biogeography of Hard Ticks, a Total Evidence Approach

CLADISTICS, Issue 1 2000
J.S.H. Klompen
Systematic relationships among the basal Ixodidae are examined using one morphological and three molecular data sets, 18S and 28S nuclear and 16S mitochondrial rDNA. Although different combinations of partitions are incompatible in a partition homogeneity test, combining them produces similar or better support for most major lineages through both additive and complementary effects. The different data sets are not complete for all taxa, but inclusion or exclusion of taxa with missing data for one or more data sets (8 of 29 ingroup taxa) does not influence overall tree topology and only weakly affects support levels. The only notable effect was based on gap treatment in the 28S data set. Gap treatment completely changes the arrangement and support levels for one basal node. The combined analyses show strong support for the Metastriata, a lineage including most endemic Australian Ixodes, and a lineage including the remaining Ixodes, but not for the Prostriata (=Ixodes s.l.). The distribution pattern of endemic Australian taxa (nearly all included in three exclusively Australian basal lineages) suggests that these lineages, and by extension the Ixodidae, originated after the isolation of Australia in the late Cretaceous, much more recently than previously indicated. [source]