Selective pressure, putative recombination events and evolutionary relationships among members of the family Closteroviridae: A proposal for a new classification

Molecular evolution of viruses is driven by both positive selection and recombination. In an effort to determine putative recombination events in the entire genome of members of the family Closteroviridae comprising 54 accessions retrieved from the international databases, a detail study was carried out by using RDP algorithm version 3.31β. Only isolates of Citrus tristeza virus and Grapevine leafroll-associated virus 3 were potential recombinants. None of members of Crinivirus genus was possible recombinant, but in turn, they were under positive selection that might be correlated with vector and/or host interactions. In contrast, Citrus tristeza virus isolates were under purifying selection as well as one-third of isolates of Grapevine leafroll-associated virus 3. The evolutionary history of all members of the Closteroviridae showed that they split into three distinct clusters corresponding to the three genera constituting this family. Moreover, the inferred phylogeny reshuffled the existing classification actually adopted by the International Committee on Taxonomy of Viruses. In this regard, each genus should be constituted by two distinct subgroups.     

Selective constraints, molecular recombination structure and phylogenetic reconstruction of isometric plant RNA viruses of the families Luteoviridae and Tymoviridae

In an effort to enhance the knowledge on molecular evolution of currently the known members of the families Luteoviridae and Tymoviridae, in-depth molecular investigations in the entire genome of 147 accessions retrieved from the international databases, were carried out. Two algorithms (RECCO and RDP version 3.31β) adapted to the mosaic structure of viruses were utilized. The recombination frequency along the sequences was dissected and demonstrated that the three virus genera of the family Luteoviridae comprise numerous members subjected to recombination. It has pointed out that the major viruses swapped a few but long genomic segments. In addition, in Barley yellow dwarf virus, heredity material might be exchanged between two different serotypes. Even more, putative recombination events occurred between two different genera. Based on Fisher’s Exact Test of Neutrality, positive selection acting on protein expression was detected only in the poleroviruses Cereal yellow dwarf virus, Potato leafroll virus and Wheat yellow dwarf virus. In contrast, several components of the family Tymoviridae were highly recombinant. Genomic portion exchange arose in many positions consisting of short fragments. Furthermore, no positive selection was detected. The evolutionary history showed, in the Luteoviridae, that all screened isolates split into three clusters corresponding to the three virus genera forming this family. Moreover, in the serotype PAV of Barley yellow dwarf virus, two major clades corresponding to PAV-USA and PAV-China, were delineated. Similarly, in the Tymoviridae, all analyzed isolates fell into four groups corresponding to the three virus genera composing this family along with the unclassified Tymoviridae. Inferred phylogenies reshuffled the existing classification and showed that Wheat yellow dwarf virus-RPV was genetically closely related to Cereal yellow dwarf virus and the unclassified Tymoviridae Grapevine syrah virus-1 constituted an integral part of the genus Marafivirus.     

5'-3' RNA-RNA interaction facilitates cap- and poly(A) tail-independent translation of tomato bushy stunt virus mrna: a potential common mechanism for tombusviridae

Tomato bushy stunt virus (TBSV) is the prototypical member of the genus Tombusvirus in the family Tombusviridae. The (+)-strand RNA genome of TBSV lacks both a 5' cap and a 3' poly(A) tail and instead contains a 3'-terminal RNA sequence that acts as a cap-independent translational enhancer (3' CITE). In this study, we have determined the RNA secondary structure of the translation-specific central segment of the 3' CITE, termed region 3.5 (R3.5). MFOLD structural modeling combined with solution structure mapping and comparative sequence analysis indicate that R3.5 adopts a branched structure that contains three major helices. Deletion and substitution studies revealed that two of these extended stem-loop (SL) structures are essential for 3' CITE activity in vivo. In particular, the terminal loop of one of these SLs, SL-B, was found to be critical for translation. Compensatory mutational analysis showed that SL-B functions by base pairing with another SL, SL3, in the 5' untranslated region of the TBSV genome. Thus, efficient translation of TBSV mRNA in vivo requires a 5'-3' RNA-RNA interaction that effectively circularizes the message. Similar types of interactions are also predicted to occur in TBSV subgenomic mRNAs between their 5' untranslated regions and the 3' CITE, and both genomic and subgenomic 5'-3' interactions are well conserved in all members of the genus Tombusvirus. In addition, a survey of other genera in Tombusviridae revealed the potential for similar 5'-3' RNA-RNA-based interactions in their viral mRNAs, suggesting that this mechanism extends throughout this large virus family.     

Comparative Genomics of <Emphasis Type="Italic">Bifidobacterium</Emphasis>, <Emphasis Type="Italic">Lactobacillus</Emphasis> and Related Probiotic Genera

Six bacterial genera containing species commonly used as probiotics for human consumption or starter cultures for food fermentation were compared and contrasted, based on publicly available complete genome sequences. The analysis included 19 Bifidobacterium genomes, 21 Lactobacillus genomes, 4 Lactococcus and 3 Leuconostoc genomes, as well as a selection of Enterococcus (11) and Streptococcus (23) genomes. The latter two genera included genomes from probiotic or commensal as well as pathogenic organisms to investigate if their non-pathogenic members shared more genes with the other probiotic genomes than their pathogenic members. The pan- and core genome of each genus was defined. Pairwise BLASTP genome comparison was performed within and between genera. It turned out that pathogenic Streptococcus and Enterococcus shared more gene families than did the non-pathogenic genomes. In silico multilocus sequence typing was carried out for all genomes per genus, and the variable gene content of genomes was compared within the genera. Informative BLAST Atlases were constructed to visualize genomic variation within genera. The clusters of orthologous groups (COG) classes of all genes in the pan- and core genome of each genus were compared. In addition, it was investigated whether pathogenic genomes contain different COG classes compared to the probiotic or fermentative organisms, again comparing their pan- and core genomes. The obtained results were compared with published data from the literature. This study illustrates how over 80 genomes can be broadly compared using simple bioinformatic tools, leading to both confirmation of known information as well as novel observations.     

Genome of invertebrate iridescent virus type 3 (mosquito iridescent virus)

Iridoviruses (IVs) are classified into five genera: Iridovirus and Chloriridovirus, whose members infect invertebrates, and Ranavirus, Lymphocystivirus, and Megalocytivirus, whose members infect vertebrates. Until now, Chloriridovirus was the only IV genus for which a representative and complete genomic sequence was not available. Here, we report the genome sequence and comparative analysis of a field isolate of Invertebrate iridescent virus type 3 (IIV-3), also known as mosquito iridescent virus, currently the sole member of the genus Chloriridovirus. Approximately 20% of the 190-kbp IIV-3 genome was repetitive DNA, with DNA repeats localized in 15 apparently noncoding regions. Of the 126 predicted IIV-3 genes, 27 had homologues in all currently sequenced IVs, suggesting a genetic core for the family Iridoviridae. Fifty-two IIV-3 genes, including those encoding DNA topoisomerase II, NAD-dependent DNA ligase, SF1 helicase, IAP, and BRO protein, are present in IIV-6 (Chilo iridescent virus, prototype species of the genus Iridovirus) but not in vertebrate IVs, likely reflecting distinct evolutionary histories for vertebrate and invertebrate IVs and potentially indicative of genes that function in aspects of virus-invertebrate host interactions. Thirty-three IIV-3 genes lack homologues in other IVs. Most of these encode proteins of unknown function but also encode IIV3-053L, a protein with similarity to DNA-dependent RNA polymerase subunit 7; IIV3-044L, a putative serine/threonine protein kinase; and IIV3-080R, a protein with similarity to poxvirus MutT-like proteins. The absence of genes present in other IVs, including IIV-6; the lack of obvious colinearity with any sequenced IV; the low levels of amino acid identity of predicted proteins to IV homologues; and phylogenetic analyses of conserved proteins indicate that IIV-3 is distantly related to other IV genera.     

Recombination and selection in the evolution of picornaviruses and other Mammalian positive-stranded RNA viruses

Picornaviridae are a large virus family causing widespread, often pathogenic infections in humans and other mammals. Picornaviruses are genetically and antigenically highly diverse, with evidence for complex evolutionary histories in which recombination plays a major part. To investigate the nature of recombination and selection processes underlying the evolution of serotypes within different picornavirus genera, large-scale analysis of recombination frequencies and sites, segregation by serotype within each genus, and sequence selection and composition was performed, and results were compared with those for other nonenveloped positive-stranded viruses (astroviruses and human noroviruses) and with flavivirus and alphavirus control groups. Enteroviruses, aphthoviruses, and teschoviruses showed phylogenetic segregation by serotype only in the structural region; lack of segregation elsewhere was attributable to extensive interserotype recombination. Nonsegregating viruses also showed several characteristic sequence divergence and composition differences between genome regions that were absent from segregating virus control groups, such as much greater amino acid sequence divergence in the structural region, markedly elevated ratios of nonsynonymous-to-synonymous substitutions, and differences in codon usage. These properties were shared with other picornavirus genera, such as the parechoviruses and erboviruses. The nonenveloped astroviruses and noroviruses similarly showed high frequencies of recombination, evidence for positive selection, and differential codon use in the capsid region, implying similar underlying evolutionary mechanisms and pressures driving serotype differentiation. This process was distinct from more-recent sequence evolution generating diversity within picornavirus serotypes, in which neutral or purifying selection was prominent. Overall, this study identifies common themes in the diversification process generating picornavirus serotypes that contribute to understanding of their evolution and pathogenicity.     

Specific binding of tombusvirus replication protein p33 to an internal replication element in the viral RNA is essential for replication

The mechanism of template selection for genome replication in plus-strand RNA viruses is poorly understood. Using the prototypical tombusvirus, Tomato bushy stunt virus (TBSV), we show that recombinant p33 replicase protein binds specifically to an internal replication element (IRE) located within the p92 RNA-dependent RNA polymerase coding region of the viral genome. Specific binding of p33 to the IRE in vitro depends on the presence of a C.C mismatch within a conserved RNA helix. Interestingly, the absence of the p33:p33/p92 interaction domain in p33 prevented specific but allowed nonspecific RNA binding, suggesting that a multimeric form of this protein is involved in the IRE-specific interaction. Further support for the selectivity of p33 binding in vitro was provided by the inability of the replicase proteins of the closely related Turnip crinkle virus and distantly related Hepatitis C virus to specifically recognize the TBSV IRE. Importantly, there was also a strong correlation between p33:IRE complex formation in vitro and viral replication in vivo, where mutations in the IRE that disrupted selective p33 binding in vitro also abolished TBSV RNA replication both in plant and in Saccharomyces cerevisiae cells. Based on these findings and the other known properties of p33 and the IRE, it is proposed that the p33:IRE interaction provides a mechanism to selectively recruit viral RNAs into cognate viral replicase complexes. Since all genera in Tombusviridae encode comparable replicase proteins, these results may be relevant to other members of this large virus family.     

A phylogenetic reappraisal of the Peltophorum group (Caesalpinieae: Leguminosae) based on the chloroplast trnL-F, rbcL and rps16 sequence data

The monophyly of the Peltophorum group, one of nine informal groups recognized by Polhill in the Caesalpinieae, was tested using sequence data from the trnL-F, rbcL, and rps16 regions of the chloroplast genome. Exemplars were included from all 16 genera of the Peltophorum group, and from 15 genera representing seven of the other eight informal groups in the tribe. The data were analyzed separately and in combined analyses using parsimony and Bayesian methods. The analysis method had little effect on the topology of well-supported relationships. The molecular data recovered a generally well-supported phylogeny with many intergeneric relationships resolved. Results show that the Peltophorum group as currently delimited is polyphyletic, but that eight genera plus one undescribed genus form a core Peltophorum group, which is referred to here as the Peltophorum group sensu stricto. These genera are Bussea, Conzattia, Colvillea, Delonix, Heteroflorum (inedit.), Lemuropisum, Parkinsonia, Peltophorum, and Schizolobium. The remaining eight genera of the Peltophorum group s.l. are distributed across the Caesalpinieae. Morphological support for the redelimited Peltophorum group and the other recovered clades was assessed, and no unique synapomorphy was found for the Peltophorum group s.s. A proposal for the reclassification of the Peltophorum group s.l. is presented.     

Rates and relations of mitochondrial genome evolution across the Echinoidea,with special focus on the superfamily Odontophora

In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular‐clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene. Major global oceanographic changes have been inferred during this time frame, potentially driving species diversification through environmental selection pressures. To test for signatures of selection acting on the mitochondria, the historical rate of gene evolution of individual MT genes was assessed through a branch‐site comparison of nonsynonymous to synonymous substitution ratios (ω). Models of positive selection and neutral evolution, as compared via a likelihood ratio test, show no evidence of strong historical positive selection on mitochondrial genes at the genesis of the Odontophora. However, while pairwise ω comparison revealed signatures of strong negative selection, relatively elevated ω values were observed within the Strongylocentrotus genus.     

The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity

The Iberian Peninsula represents a hot spot of cyphophthalmid (mite harvestman) disparity, with four of the eight genera currently recognized in the family Sironidae represented in the region – a generic diversity and morphological disparity not found in any other region of the World so far. From these, two genera (Iberosiro and Odontosiro) are monotypic, and are restricted to the western side of the peninsula. Parasiro is restricted to the north‐east region, from the Catalonian Coastal Ranges and both sides of the Eastern Pyrenees, in areas where the annual rainfall surpasses 1000 mm, and mostly restricted to areas with Paleozoic and Variscan rocks, with other species of the genus extending to Corsica, Sardinia, and the Italian Peninsula. A second species of the genus Paramiopsalis, Paramiopsalis eduardoi sp. nov. from Fragas do Eume, is described here along with a re‐diagnosis of the genus. Paramiopsalis species, together with Odontosiro, inhabit the north‐west corner of the Iberian Peninsula, an area with some of the highest recorded annual rainfall, and with Paleozoic rocks from the Iberian Massif or Variscan granitoid rocks. A phylogenetic analysis of the members of the family Sironidae using four molecular markers, despite not including all of the Iberian genera, clearly shows the non‐monophyly of the Iberian Cyphophthalmi, indicating that the Iberian Peninsula is home to multiple ancient lineages of mite harvestmen. The two Paramiopsalis species form a sister clade to the Balkan genus Cyphophthalmus, whereas Parasiro constitutes the first lineage of the sironids represented.     

Genus-specific localization of the TaiI family of tandem-repetitive sequences in either the centromeric or subtelomeric regions in Triticeae species (Poaceae) and its evolution in wheat.

The TaiI family sequences are classified as tandem repetitive DNA sequences present in the genome of tribe Triticeae, and are localized in the centromeric regions of common wheat, but in the subtelomeric heterochromatic regions of Leymus racemosus and related species. In this study, we investigated the chromosomal distribution of TaiI family sequences in other Triticeae species. The results demonstrated a centromeric localization in genera Triticum and Aegilops and subtelomeric localization in other genera, thus showing a genus-dependent localization of TaiI family sequences in one or the other region. The copy numbers of TaiI family sequences in species in the same genus varied greatly, whether in the centromeric or subtelomeric regions (depending on genus). We also examined the evolution of TaiI family sequences during polyploidization of hexaploid common wheat. A comparison of chromosomal locations of the major TaiI family signals in common wheat and in its ancestral species suggested that the centromeric TaiI family sequences in common wheat were inherited from its ancestors with little modification, whereas a mixed origin for the B genome of common wheat was indicated.     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.     

Phylogenetic analysis of the genera Pseudonocardia and Actinobispora based on 16S ribosomal DNA sequences

The 16S rDNA sequences of 11 strains, nine type strains of validated Pseudonocardia species and Actinobispora yunnanensis, and two strains of unnamed Pseudonocardia species, were determined and compared with those of representatives of the family Pseudonocardiaceae. The phylogenetic analysis indicated that all of the validated species of the genera Pseudonocardia and Actinobispora consistently formed a monophyletic unit and separated well from the other genera of the family Pseudonocardiaceae. One unnamed Pseudonocardia strain was related to members of the genus Pseudonocardia, whereas the other unnamed Pseudonocardia strain formed a distinct clade within the radiation of the genus Amycolatopsis.     

NUCLEAR DNA CONTENT VARIATION WITHIN THE ROSACEAE

Nuclear DNA content has been estimated using flow cytometry for 17 species and eight cultivars of Malus and for 44 species of 29 other genera within the Rosaceae. Compared to other angiosperms, diploid genome sizes vary little within the family Rosaceae and within the genus Malus. C-values of genera within the subfamilies Spiraeoideae and Rosoideae are among the smallest of flowering plants thus far reported. In general, the Maloideae have the largest diploid genomes of the family, consistent with their higher chromosome numbers and presumed polyploid origin.     

A Preliminary Study on the Taxonomy of the Family Magnoliaceae

A new system of classification of Magnoliaceae proposed. This paper deals mainly with taxonomy and phytogeography of the family Magnoliaceae on the basis of external morphology, wood anatomy and palynology. Different authors have had different ideas about the delimitation of genera of this family, their controversy being carried on through more than one hundred years (Table I). Since I have been engaged in the work of the Flora Reipublicae Popularis Sinicae, I have accumulated a considerable amount of information and material and have investigated the living plants at their natural localities, which enable me to find out the evolutionary tendencies and primitive morphological characters of various genera of the family. According to the evolutionary tendencies of the characters and the geographical distribution of this family I propose a new system by dividing it into two subfamilies, Magnolioideae and Liriodendroideae Law (1979), two tribes, Magnolieae and Michelieae Law, four subtribes, Manglietiinae Law, Magnoliinae, Elmerrilliinae Law and Micheliinae, and fifteen genera (Fig. 1 ), a system which is different from those by J. D. Dandy (1964-1974) and the other authors. The recent distribution and possible survival centre of Magnoliaceae. The members of Magnoliaceae are distributed chiefly in temperate and tropical zones of the Northern Hemisphere, ——Southeast Asia and southeast North America, but a few genera and species also occur in the Malay Archipelago and Brazil of the Southern Hemisphere. Forty species of 4 genera occur in America, among which one genus (Dugendiodendron) is endemic to the continent, while about 200 species of 14 genera occur in Southeast Asia, of which 12 genera are endemic. In China there are about 110 species of 11 genera which mostly occur in Guangxi, Guangdong and Yunnan; 58 species and more than 9 genera occur in the mountainous districts of Yunnan. Moreover, one genus (Manglietiastrum Law, 1979) and 19 species are endemic to this region. The family in discussion is much limited to or interruptedly distributed in the mountainous regions of Guangxi, Guangdong and Yunnan. The regions are found to have a great abundance of species, and the members of the relatively primitive taxa are also much more there than in the other regions of the world. The major genera, Manglietia, Magnolia and Michelia, possess 160 out of a total of 240 species in the whole family. Talauma has 40 species, while the other eleven genera each contain only 2 to 7 species, even with one monotypic genus. These three major genera are sufficient for indicating the evolutionary tendency and geographical distribution of Magnoliaceae. It is worthwhile discussing their morphological characters and distributional patterns as follows: The members of Manglietia are all evergreen trees, with flowers terminal, anthers dehiscing introrsely, filaments very short and flat, ovules 4 or more per carpel. This is considered as the most primitive genus in subtribe Manglietiinae. Eighteen out of a total of 35 species of the genus are distributed in the western, southwest to southeast Yunnan. Very primitive species, such as Manglietia hookeri, M. insignis and M. megaphylla, M. grandis, also occur in this region. They are distributed from Yunnan eastwards to Zhejiang and Fujian through central China, south China, with only one species (Manglietia microtricha) of the genus westwards to Xizang. There are several species distributing southwards from northeast India to the Malay Archipelago (Fig. 7). The members of Magnolia are evergreen and deciduous trees or shrubs, with flowers terminal, anthers dehiscing introrsely or laterally, ovules 2 per carpel, stipule adnate to the petiole. The genus Magnolia is the most primitive in the subtribe Magnoliinae and is the largest genus of the family Magnoliaceae. Its deciduous species are distributed from Yunnan north-eastwards to Korea and Japan (Kurile N. 46’) through Central China, North China and westwards to Burma, the eastern Himalayas and northeast India. The evergreen species are distributed from northeast Yunnan (China) to the Malay Archipelago. In China there are 23 species, of which 15 seem to be very primitive, e.g. Magnolia henryi, M. delavayi, M. officinalis and M. rostrata, which occur in Guangxi, Guangdong and Yunnan. The members of Michelia are evergreen trees or shrubs, with flowers axillary, anthers dehiscing laterally or sublaterally, gynoecium stipitate, carpels numerous or few. Michelia is considered to be the most primitive in the subtribe Micheliinae, and is to the second largest genus of the family. About 23 out of a total of 50 species of this genus are very primitive, e.g. Michelia sphaerantha, M. lacei, M. champaca, and M. flavidiflora, which occur in Guangdong, Guangxi and Yunnan (the distributional center of the family under discussion) and extend eastwards to Taiwan of China, southern Japan through central China, southwards to the Malay Archipelago through Indo-China. westwards to Xizang of China, and south-westwards to India and Sri Lanka (Fig. 7). The members of Magnoliaceae are concentrated in Guangxi, Guangdong and Yunnan and radiate from there. The farther away from the centre, the less members we are able to find, but the more advanced they are in morphology. In this old geographical centre there are more primitive species, more endemics and more monotypic genera. Thus it is reasonable to assume that the region of Guangxi, Guangdong and Yunnan, China, is not only the centre of recent distribution, but also the chief survival centreof Magnoliaceae in the world.     

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113)

Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Phylogeny of the shore crab family Grapsidae (Decapoda: Brachyura: Thoracotremata) based on a multilocus approach

The Grapsidae are a thoracotreme crab family with 40 species in eight genera (in their strict definition), and possess a number of morphological and molecular synapomorphies. Previous phylogenetic studies based on mitochondrial DNA markers established the monophyly of this family, but suggested possible paraphyly or polyphyly of some of the constituent genera. To test the validity of previous hypotheses, the present study reconstructed a molecular phylogeny of the grapsid crabs based on five molecular markers, including mitochondrial DNA markers and the first use of nuclear protein‐coding markers to address this issue. Monophyly of Grapsidae was confirmed, with the exception of the position of the monotypic genus Leptograpsodes. The polyphyly of the genus Pachygrapsus is consistent with previous molecular phylogenies, as members from this genus are dispersed throughout our gene tree. Grapsus and Planes were shown to be paraphyletic, with species of Pachygrapsus nested within them. Our study found incongruences between the currently adopted classification of the family, and hence taxonomic revisions will be needed. We hereby demonstrate the use of nuclear protein‐coding markers for high confidence reconstruction of decapod phylogenies, resolving most of the early splits that mitochondrial DNA markers alone are unable to tackle. © 2015 The Linnean Society of London     

Three-dimensional reconstruction of hibiscus chlorotic ringspot virus

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense, single-stranded RNA virus, which belongs to the Tombusviridae family and infects plants of the Hibiscus genus, including kenaf, a woody plant of agricultural importance. These icosahedral viruses have a capsid consisting of 180 copies of coat protein (CP) arranged with T=3 symmetry. The CP consists of an internal RNA-binding domain, a shell-forming domain and a protruding domain. The HCRSV virion was reconstructed to about 12A resolution from cryo-EM images using the program EMAN. The structure had the arrangement of 90 dimers of protruding domains characteristic of the Tombusviridae. Reconstructions were also made from negatively stained samples, and showed essentially the same features. In addition, a particle of a different, "smooth" appearance was also identified in the negatively stained samples. These particles were slightly smaller and lacked protruding domains. Biochemical analysis confirmed the presence of two protein products: a 37 kDa protein identified as HCRSV CP and a 54 kDa protein that appeared to be of non-HCRSV origin.     

Searching for evidence of positive selection in the human genome using patterns of microsatellite variability

Both natural selection and nonequilibrium population-level processes can lead to a skew in the frequency distribution of polymorphisms. Population-level processes are expected to affect all loci in a roughly equal fashion, whereas selection will affect only some regions of the genome. We conducted a sliding-window analysis of the frequency distribution of microsatellite polymorphisms across the human genome to identify regions that may be under positive selection. The analysis was based on a published data set of 5,257 mapped microsatellites in individuals of European ancestry. Observed and expected numbers of alleles were compared under a stepwise mutation model (SMM) using analytical formulae. Observed and expected heterozygosities were compared under a SMM using coalescent simulations. The two sets of analyses gave similar results. Approximately one-fourth of all loci showed a significant deficit of heterozygosity, consistent with a recent population expansion. Forty-three windows were identified with extreme skews in the frequency distribution of polymorphisms (in the direction of a deficit of heterozygosity, given the number of alleles). If these extreme windows are tracking selection at linked sites, theory predicts that they should be more common in regions of the genome with less recombination. We tested this prediction by comparing recombination rates in these extreme windows and in other regions of the genome and found that extreme windows had a significantly lower recombination rate than the genomic average. The proportion of extreme windows was significantly higher on the X chromosome than on the autosomes. Moreover, all the windows with extreme skews on the X chromosome were found in two clusters near the centromere; both these clusters exhibit markedly reduced recombination rates. These analyses point to regions of the genome that may recently have been subject to positive selection. These results also suggest that the effects of positive selection may be more pronounced on the X chromosome than on the autosomes in humans.