Postsymbiotic plasmid acquisition and evolution of the repA1-replicon in Buchnera aphidicola

Buchnera aphidicola is an obligate, strictly vertically transmitted, bacterial symbiont of aphids. It supplies its host with essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. Several lineages of Buchnera show adaptation to their nutritional role in the form of plasmid-mediated amplification of key-genes involved in the biosynthesis of tryptophan (trpEG) and leucine (leuABCD). Phylogenetic analyses of these plasmid-encoded functions have thus far suggested the absence of horizontal plasmid exchange among lineages of Buchnera. Here, we describe three new Buchnera plasmids, obtained from species of the aphid host families Lachnidae and Pemphigidae. All three plasmids belong to the repA1 family of Buchnera plasmids, which is characterized by the presence of a repA1-replicon responsible for replication initiation. A comprehensive analysis of this family of plasmids unexpectedly revealed significantly incongruent phylogenies for different plasmid and chromosomally encoded loci. We infer from these incongruencies a case of horizontal plasmid transfer in Buchnera. This process may have been mediated by secondary endosymbionts, which occasionally undergo horizontal transmission in aphids.

Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes

Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1 000 000 hits from 462 500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

Speciation through homoploid hybridization between allotetraploids in peonies (Paeonia)

Phylogenies of Adh1 and Adh2 genes suggest that a widespread Mediterranean peony, Paeonia officinalis, is a homoploid hybrid species between two allotetraploid species, Paeonia peregrina and a member of the Paeonia arietina species group. Three phylogenetically distinct types of Adh sequences have been identified from both accessions of P. officinalis, of which two types are most closely related to the two homoeologous Adh loci of the P. arietina group and the remaining type came from one of the two Adh homoeologs of P. peregrina. The other Adh homoeolog of P. peregrina was apparently lost from the hybrid genome, possibly through backcrossing with the P. arietina group. This is a documentation of homoploid hybrid speciation between allotetraploid species in nature. This study suggests that hybrid speciation between allotetraploids can occur without an intermediate stage of genome diploidization or a further doubling of genome size.

Integrated fossil and molecular data reconstruct bat echolocation

Molecular and morphological data have important roles in illuminating evolutionary history. DNA data often yield well resolved phylogenies for living taxa, but are generally unattainable for fossils. A distinct advantage of morphology is that some types of morphological data may be collected for extinct and extant taxa. Fossils provide a unique window on evolutionary history and may preserve combinations of primitive and derived characters that are not found in extant taxa. Given their unique character complexes, fossils are critical in documenting sequences of character transformation over geologic time and may elucidate otherwise ambiguous patterns of evolution that are not revealed by molecular data alone. Here, we employ a methodological approach that allows for the integration of molecular and paleontological data in deciphering one of the most innovative features in the evolutionary history of mammals—laryngeal echolocation in bats. Molecular data alone, including an expanded data set that includes new sequences for the A2AB gene, suggest that microbats are paraphyletic but do not resolve whether laryngeal echolocation evolved independently in different microbat lineages or evolved in the common ancestor of bats and was subsequently lost in megabats. When scaffolds from molecular phylogenies are incorporated into parsimony analyses of morphological characters, including morphological characters for the Eocene taxa Icaronycteris, Archaeonycteris, Hassianycteris, and Palaeochiropteryx, the resulting trees suggest that laryngeal echolocation evolved in the common ancestor of fossil and extant bats and was subsequently lost in megabats. Molecular dating suggests that crown-group bats last shared a common ancestor 52 to 54 million years ago.

A general additive distance with time-reversibility and rate variation among nucleotide sites.

As additivity is a very useful property for a distance measure, a general additive distance is proposed under the stationary time-reversible (SR) model of nucleotide substitution or, more generally, under the stationary, time-reversible, and rate variable (SRV) model, which allows rate variation among nucleotide sites. A method for estimating the mean distance and the sampling variance is developed. In addition, a method is developed for estimating the variance-covariance matrix of distances, which is useful for the statistical test of phylogenies and molecular clocks. Computer simulation shows (i) if the sequences are longer than, say, 1000 bp, the SR method is preferable to simpler methods; (ii) the SR method is robust against deviations from time-reversibility; (iii) when the rate varies among sites, the SRV method is much better than the SR method because the distance is seriously underestimated by the SR method; and (iv) our method for estimating the sampling variance is accurate for sequences longer than 500 bp. Finally, a test is constructed for testing whether DNA evolution follows a general Markovian model.

Phylogenetic resolution within the Elephantidae using fossil DNA sequence from the American mastodon (Mammut americanum) as an outgroup.

DNA was extracted from the extinct American mastodon, the extinct woolly mammoth, and the modern Asian and African elephants to test the traditional morphologically based phylogeny within Elephantidae. Phylogenetic analyses of the aligned sequences of the mitochondrial gene cytochrome b support a monophyletic Asian elephant-woolly mammoth clade when the American mastodon is used as an outgroup. Previous molecular studies were unable to resolve the relationships of the woolly mammoth, Asian elephant, and African elephant because the sequences appear to have evolved at heterogeneous rates and inappropriate outgroups were used for analysis. The results demonstrate the usefulness of fossil molecular data from appropriate sister taxa for resolving phylogenies of highly derived or early radiating lineages.

ndhF sequence evolution and the major clades in the sunflower family.

An extensive sequence comparison of the chloroplast ndhF gene from all major clades of the largest flowering plant family (Asteraceae) shows that this gene provides approximately 3 times more phylogenetic information than rbcL. This is because it is substantially longer and evolves twice as fast. The 5' region (1380 bp) of ndhF is very different from the 3' region (855 bp) and is similar to rbcL in both the rate and the pattern of sequence change. The 3' region is more A+T-rich, has higher levels of nonsynonymous base substitution, and shows greater transversion bias at all codon positions. These differences probably reflect different functional constraints on the 5' and 3' regions of ndhF. The two patterns of base substitutions of ndhF are particularly advantageous for phylogenetic reconstruction because the conserved and variable segments can be used for older and recent groups, respectively. Phylogenetic analyses of 94 ndhF sequences provided much better resolution of relationships than previous molecular and morphological phylogenies of the Asteraceae. The ndhF tree identified five major clades: (i) the Calyceraceae is the sister family of Asteraceae; (ii) the Barnadesioideae is monophyletic and is the sister group to the rest of the family; (iii) the Cichorioideae and its two basal tribes Mutisieae and Cardueae are paraphyletic; (iv) four tribes of Cichorioideae (Lactuceae, Arctoteae, Liabeae, and Vernonieae) form a monophyletic group, and these are the sister clade of the Asteroideae; and (v) the Asteroideae is monophyletic and includes three major clades.

In vivo regulation of muscle glycogen synthase and the control of glycogen synthesis.

The activity of glycogen synthase (GSase; EC 2.4.1.11) is regulated by covalent phosphorylation. Because of this regulation, GSase has generally been considered to control the rate of glycogen synthesis. This hypothesis is examined in light of recent in vivo NMR experiments on rat and human muscle and is found to be quantitatively inconsistent with the data under conditions of glycogen synthesis. Our first experiments showed that muscle glycogen synthesis was slower in non-insulin-dependent diabetics compared to normals and that their defect was in the glucose transporter/hexokinase (GT/HK) part of the pathway. From these and other in vivo NMR results a quantitative model is proposed in which the GT/HK steps control the rate of glycogen synthesis in normal humans and rat muscle. The flux through GSase is regulated to match the proximal steps by "feed forward" to glucose 6-phosphate, which is a positive allosteric effector of all forms of GSase. Recent in vivo NMR experiments specifically designed to test the model are analyzed by metabolic control theory and it is shown quantitatively that the GT/HK step controls the rate of glycogen synthesis. Preliminary evidence favors the transporter step. Several conclusions are significant: (i) glucose transport/hexokinase controls the glycogen synthesis flux; (ii) the role of covalent phosphorylation of GSase is to adapt the activity of the enzyme to the flux and to control the metabolite levels not the flux; (iii) the quantitative data needed for inferring and testing the present model of flux control depended upon advances of in vivo NMR methods that accurately measured the concentration of glucose 6-phosphate and the rate of glycogen synthesis.

Flightless brown kiwis of New Zealand possess extremely subdivided population structure and cryptic species like small mammals.

Using allozymes and mtDNA sequences from the cytochrome b gene, we report that the brown kiwi has the highest levels of genetic structuring observed in birds. Moreover, the mtDNA sequences are, with two minor exceptions, diagnostic genetic markers for each population investigated, even though they are among the more slowly evolving coding regions in this genome. A major unexpected finding was the concordant split in molecular phylogenies between brown kiwis in the southern South Island and elsewhere in New Zealand. This basic phylogeographic boundary halfway down the South Island coincides with a fixed allele difference in the Hb nuclear locus and strongly suggests that two morphologically cryptic species are currently merged under one polytypic species. This is another striking example of how molecular genetic assays can detect phylogenetic discontinuities that are not reflected in traditional morphologically based taxonomies. However, reanalysis of the morphological characters by using phylogenetic methods revealed that the reason for this discordance is that most are primitive and thus are phylogenetically uninformative. Shared-derived morphological characters support the same relationships evident in the molecular phylogenies and, in concert with the molecular data, suggest that as brown kiwis colonized northward from the southern South Island, they retained many primitive characters that confounded earlier systematists. Strong subdivided population structure and cryptic species in brown kiwis seem to have evolved relatively recently as a consequence of Pleistocene range disjunctions, low dispersal power, and genetic drift in small populations.

Multiple origins of the yucca-yucca moth association.

The association of species of yucca and their pollinating moths is considered one of the two classic cases of obligate mutualism between floral hosts and their pollinators. The system involves the active collection of pollen by females of two prodoxid moth genera and the subsequent purposeful placement of the pollen on conspecific stigmas of species of Yucca. Yuccas essentially depend on the moths for pollination and the moths require Yucca ovaries for oviposition. Because of the specificity involved, it has been assumed that the association arose once, although it has been suggested that within the prodoxid moths as a whole, pollinators have arisen from seed predators more than once. We show, by using phylogenies generated from three molecular data sets, that the supposed restriction of the yucca moths and their allies to the Agavaceae is an artifact caused by an incorrect circumscription of this family. In addition we provide evidence that Yucca is not monophyletic, leading to the conclusion that the modern Yucca-yucca moth relationship developed independently more than once by colonization of a new host.

Direct evidence for secondary loss of mitochondria in Entamoeba histolytica.

Archezoan protists are though to represent lineages that diverged from other eukaryotes before acquisition of the mitochondrion and other organelles. The parasite Entamoeba histolytica was originally included in this group. Ribosomal RNA based phylogenies, however, place E. histolytica on a comparatively recent branch of the eukaryotic tree, implying that its ancestors had these structures. In this study, direct evidence for secondary loss of mitochondrial function was obtained by isolating two E. histolytica genes encoding proteins that in other eukaryotes are localized in the mitochondrion: the enzyme pyridine nucleotide transhydrogenase and the chaperonin cpn60. Phylogenetic analysis of the E. histolytica homolog of cpn60 confirmed that it is specifically related to the mitochondrial lineage. The data suggest that a mitochondrial relic may persist in this organism. Similar studies are needed in archezoan protists to ascertain which, if any, eukaryotic lineages primitively lack mitochondria.

Evidence from molecular systematics for decreased avian diversification in the pleistocene Epoch.

Pleistocene glaciations have been suggested as major events influencing speciation rates in vertebrates. Avian paleontological studies suggest that most extant species evolved in the Pleistocene Epoch and that species' durations decreased through the Pleistocene because of heightened speciation rates. Molecular systematic studies provide another data base for testing these predictions. In particular, rates of diversification can be determined from molecular phylogenetic trees. For example, an increasing rate of speciation (but constant extinction) requires shorter intervals between successive speciation events on a phylogenetic tree. Examination of the cumulative distribution of reconstructed speciation events in mtDNA phylogenies of 11 avian genera, however, reveals longer intervals between successive speciation events as the present time is approached, suggesting a decrease in net diversification rate through the Pleistocene Epoch. Thus, molecular systematic studies do not indicate a pulse of Pleistocene diversification in passerine birds but suggest, instead, that diversification rates were lower in the Pleistocene than for the preceding period. Documented habitat shifts likely led to the decreased rate of diversification, although from molecular evidence we cannot discern whether speciation rates decreased or extinction rates increased.

Cell-surface-expressed T-cell antigen-receptor zeta chain is associated with the cytoskeleton.

The T-cell antigen receptor zeta chain plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. zeta chain can associate with certain protein tyrosine kinases and retains the capacity to transduce signals independently of the other receptor subunits. Thus, zeta chain could couple cell-surface-expressed T-cell antigen receptors to the intracellular signal-transduction apparatus by its association with various intracellular molecules in addition to tyrosine kinases. In the process of searching for zeta chain-associated molecules we observed that after lysis of resting T cells with Triton X-100, zeta chain is localized in the detergent-insoluble fraction, in addition to its presence in the detergent-soluble fraction. Treatment of T cells with cytochalasin B, an actin-depolymerizing agent, leads to the complete dissociation of zeta chain from the Triton-insoluble fraction, suggesting a linkage between zeta chain and the cytoskeletal matrix. We have also determined that cytoskeletal-associated zeta chain is expressed on the cell surface. Furthermore, a tyrosine-phosphorylated 16-kDa zeta chain was detected only in the Triton-insoluble cytoskeletal fraction of resting T cells. zeta chain also maintains its association with the cytoskeleton when expressed in COS cells, inferring that the cytoskeletal elements involved in this linkage may be ubiquitous. Finally, we have localized a 42-amino acid region in the intracytoplasmic domain of zeta chain, which is crucial for maximal interaction between zeta chain and the cytoskeleton. Anchorage of cell-surface-expressed zeta chain to the cytoskeleton in resting T cells may facilitate recycling of receptor complexes and/or allow the transduction of external stimuli into the cell.

Relações filogenéticas das espécies de Crenicichla Heckel, 1840 e Teleocichla Kullander, 1988 (Teleostei: Cichlidae)

São reconhecidos 90 nomes específicos válidos de Crenicichla e oito de Teleocichla. Juntos, os dois gêneros-alvo do presente estudo compreendem quase 1/5 da diversidade total de Cichlinae, subfamília neotropical de Cichlidae. Apesar das espécies de Crenicichla e Teleocichla formarem um clado bem corroborado através de filogenias baseadas tanto em dados morfológicos quanto em dados moleculares, as relações entre as suas espécies foram ainda pouco estudadas. Os dois estudos filogenéticos de Crenicichla conhecidos são parcialmente discordantes entre si e incorporaram apenas uma parcela da diversidade do grupo. Baseados apenas em dados moleculares, não foram acompanhados por um estudo de caracteres morfológicos que indicariam as sinapomorfias ou características diagnósticas para identificação dos grupos monofiléticos delimitados. No presente estudo, os principais objetivos consistem em testar o monofiletismo do grupo formado pelas espécies de Crenicichla e Teleocichla e identificar e definir unidades monofiléticas dentro desse grupo, com base na análise cladística de caracteres morfológicos. Como objetivo secundário, são testadas as recentes hipóteses de relações filogenéticas dessas espécies com as demais espécies de ciclídeos neotropicais. Foram incluídas todas as espécies válidas de Teleocichla e 54 espécies válidas de Crenicichla (60% das espécies válidas), além de uma espécie nova de Teleocichla e cinco prováveis espécies novas de Crenicichla. 20 representantes de diferentes linhagens de Cichlinae foram incluídos, totalizando 88 táxons terminais. As análises cladísticas foram realizadas a partir de uma matriz com 211 caracteres provenientes do estudo comparado de morfologia externa, incluindo padrões de colorido e osteologia. Além da análise com pesagens igualitárias, foram explorados também os resultados das análises com pesagem implícita utilizando diferentes valores da variável k e com pesagem sucessiva. A partir da comparação e discussão dos resultados obtidos a partir das diferentes análises, a topologia obtida através da análise com pesagem implícita utilizando o valor de k=3 foi escolhida para obtenção das inferências filogenéticas. Duas classificações alternativas foram discutidas e, a fim de minimizar mudanças nomenclaturais, aquela baseada no reconhecimento de subgêneros de Crenicichla correspondendo aos grupos monofiléticos encontrados foi preferida em detrimento da proposta baseada no reconhecimento de vários gêneros. Isso porque o posicionamento de Crenicichla macrophthalma (espécie-tipo de Crenicichla) continua sendo considerado instável. O gênero Crenicichla é corroborado como um grande clado formado por todas as espécies de Crenicichla e Teleocichla incluídas e é sustentado por 40 sinapomorfias não-ambíguas. Um complexo cenário foi encontrado quanto às relações entre as espécies de Crenicichla, com várias linhagens dentro desse grande grupo, assim como era previsto de acordo com estudos filogenéticos prévios. As relações entre essas linhagens, por outro lado, são ainda instáveis, podendo variar de acordo com os diferentes tipos de pesagem aplicados e apresentam algumas divergências em relação aos estudos prévios, que também divergem entre si. Teleocichla é um grupo monofilético dentro de Crenicichla e foi considerado como um de seus oito subgêneros. O subgênero Crenicichla é constituído apenas por Crenicichla macrophthalma. Os seis subgêneros restantes (Wallaciia, Batrachops, Hemeraia, Saxatilia, Lugubria e Lacustria) correspondem totalmente ou parcialmente a grupos de espécies de Crenicichla previamente existentes na literatura. Em Lacustria, quatro complexos de espécies foram delimitados: C. missioneira, C. scotti, C. jaguarensis e C. lacustris sensu stricto. Foram listadas as espécies nominais de cada subgênero e uma diagnose para auxiliar a identificação dos mesmos foi elaborada. Uma nova hipótese de relações de Crenicichla em Cichlinae é inferida a partir da análise realizada, na qual Crenicichla é grupo-irmão de um clado formado por Chaetobranchus flavescens e todos os representantes de Cichlasomatini e Geophagini incluídos