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Highlights: [•] PNP2 and RPH are sister taxa which arose through duplication of the ancestral PNP1 domain. [•] Branch and site-specific dN/dS analyses show that PNP and RPH domains have undergone directional sequence change. [•] Codons showing dN/dS ratios >1.0 are outside the ordered regions. [Copyright &y& Elsevier]

Human papillomavirus type 18 (HPV18) and HPV45 account for approximately 20% of all cervix cancers. We show that HPV18, HPV45, and the recently discovered HPV97 comprise a clade sharing a most recent common ancestor within HPV α7 species. Variant lineages of these HPV types were classified by sequence analysis of the upstream regulatory region/E6 region among cervical samples from a population-based study in Costa Rica, and 27 representative genomes from each major variant lineage were sequenced. Nucleotide variation within HPV18 and HPV45 was 3.82% and 2.39%, respectively, and amino acid variation was 4.73% and 2.87%, respectively. Only 18 nucleotide variations, of which 10 were nonsynonymous, were identified among three HPV97 genomes. Full-genome comparisons revealed maximal diversity between HPV18 African and non-African variants (2.6% dissimilarity), whereas HPV18 Asian-American [E1 (AA)] and European (E2) variants were closely related (less than 0.5% dissimilarity); HPV45 genomes had a maximal difference of 1.6% nucleotides. Using a Bayesian Markov chain Monte Carlo (MCMC) method, the divergence times of HPV18, -45, and -97 from their most recent common ancestors indicated that HPV18 diverged approximately 7.7 million years (Myr) ago, whereas HPV45 and HPV97 split off around 5.7 Myr ago, in a period encompassing the divergence of the great ape species. Variants within the HPV18/45/97 lineages were estimated to have diverged from their common ancestors in the genus Homo within the last 1 Myr (<0.7 Myr). To investigate the molecular basis of HPV18, HPV45, and HPV97 evolution, regression models of codon substitution were used to identify lineages and amino acid sites under selective pressure. The E5 open reading frame (ORF) of HPV18 and the E4 ORFs of HPV18, HPV45, and HPV18/45/97 had nonsynonymous/synonymous substitution rate ratios (dN/dS) over 1 indicative of positive Darwinian selection. The L1 ORF of HPV18 genomes had an increased proportion of nonsynonymous substitutions (4.93%; average dN/dS ratio [M3] = 0.3356) compared to HPV45 (1.86%; M3 = 0.1268) and HPV16 (2.26%; M3 = 0.1330) L1 ORFs. In contrast, HPV18 and HPV16 genomes had similar amino acid substitution rates within the E1 ORF (2.89% and 3.24%, respectively), while HPV45 E1 was highly conserved (amino acid substitution rate was 0.77%). These data provide an evolutionary history of this medically important clade of HPVs and identify an unexpected divergence of the L1 gene of HPV18 that may have clinical implications for the long-term use of an L1-virus-like particle-based prophylactic vaccine. [ABSTRACT FROM AUTHOR]

The 'crisis discipline' of conservation biology has voraciously incorporated many technologies to speed up and increase the accuracy of conservation decision-making. Genetic approaches to characterizing endangered species or areas that contain endangered species are prime examples of this. Technical advances in areas such as high-throughput sequencing, microsatellite analysis and non-invasive DNA sampling have led to a much-expanded role for genetics in conservation. Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes. [ABSTRACT FROM AUTHOR]

The article presents a perspective on the comparison between species discovery and species identification in DNA barcoding. The problems with DNA barcodes and species has been at the heart of the discussion at the several meetings that have been held on DNA barcoding. According to the author, species identification, which comes after established taxonomy, should be the domain of DNA barcoding. Furthermore, DNA sequence information can never be used by itself as an indicator of species boundaries.

The article discusses various reports published within the issue, including one on how mitochondria has played a primary role in how scientists understand the organic world, on the description of the mitochondrial function from a genomic view, and on the different approaches of DNA sequence-based research.

Background: The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. Results: We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. Conclusions: We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. [ABSTRACT FROM AUTHOR]

Abstract: Suprafamilial relationships among characiform fishes and implications for the taxonomy and biogeographic history of the Characiformes were investigated by parsimony analysis of four nuclear and two mitochondrial genes across 124 ingroup and 11 outgroup taxa. Simultaneous analysis of 3660 aligned base pairs from the mitochondrial 16S and cytochrome b genes and the nuclear recombination activating gene (RAG2), seven in absentia (sia), forkhead (fkh), and α-tropomyosin (trop) gene loci confirmed the non-monophyly of the African and Neotropical assemblages and corroborated many suprafamilial groups proposed previously on the basis of morphological features. The African distichodontids plus citharinids were strongly supported as a monophyletic Citharinoidei that is the sistergroup to all other characiforms, which form a monophyletic Characoidei composed of two large clades. The first represents an assemblage of both African and Neotropical taxa, wherein a monophyletic African Alestidae is sister to a smaller clade comprised of the Neotropical families Ctenolucidae, Lebiasinidae, and the African Hepsetidae, with that assemblage sister to a strictly Neotropical clade comprised of the Crenuchidae and Erythrinidae. The second clade within the Characoidei is strictly Neotropical and includes all other Characiformes grouped into two well supported major clades. The first, corresponding to a traditional definition of the Characidae, is congruent with some groupings previously supported by morphological evidence. The second clade comprises a monophyletic Anostomoidea that is sister to a clade formed by the families Hemiodontidae, Parodontidae, and Serrasalmidae, with that assemblage, in turn, the sistergroup of the Cynodontidae. Serrasalmidae, traditionally regarded as a subfamily of Characidae, was recovered as the sistergroup of (Anostomoidea (Parodontidae+Hemiodontidae)) and the family Cynodontidae was recovered with strong support as the sistergroup to this assemblage. Our results reveal three instances of trans-continental sistergroup relationships and, in light of the fossil evidence, suggest that marine dispersal cannot be ruled out a priori and that a simple model of vicariance does not readily explain the biogeographic history of the characiform fishes. [Copyright &y& Elsevier]

To investigate population differentiation in a comparative and historical context, segments of the mitochondrial cytochrome c oxidase subunit I gene and the control region were sequenced in Panulirus argus from nine sites along approximately 1,500 km of the Northern Caribbean Sea ( n = 326) and analyzed with respect to available panulirid data. A mismatch analysis and Fu's F test uncovered a signature of historical population expansion around the time of the Last Glacial Maximum. Significant population structure was not detected in the area. The data supported a hypothesis of panmixia resulting from ongoing larval transport by ocean currents and historical population expansion. Despite high intraspecific divergence levels at COI within Panulirus argus and several other Panulirus species, genetic species identification through DNA barcoding was feasible using either a modified distance threshold or a character-based approach. [ABSTRACT FROM AUTHOR]

Background: Human Papillomavirus type 16 (HPV16) causes over half of all cervical cancer and some HPV16 variants are more oncogenic than others. The genetic basis for the extraordinary oncogenic properties of HPV16 compared to other HPVs is unknown. In addition, we neither know which nucleotides vary across and within HPV types and lineages, nor which of the single nucleotide polymorphisms (SNPs) determine oncogenicity. Methods: A reference set of 62 HPV16 complete genome sequences was established and used to examine patterns of evolutionary relatedness amongst variants using a pairwise identity heatmap and HPV16 phylogeny. A BLAST-based algorithm was developed to impute complete genome data from partial sequence information using the reference database. To interrogate the oncogenic risk of determined and imputed HPV16 SNPs, odds-ratios for each SNP were calculated in a case-control viral genome-wide association study (VWAS) using biopsy confirmed high-grade cervix neoplasia and self-limited HPV16 infections from Guanacaste, Costa Rica. Results: HPV16 variants display evolutionarily stable lineages that contain conserved diagnostic SNPs. The imputation algorithm indicated that an average of 97.5±1.03% of SNPs could be accurately imputed. The VWAS revealed specific HPV16 viral SNPs associated with variant lineages and elevated odds ratios; however, individual causal SNPs could not be distinguished with certainty due to the nature of HPV evolution. Conclusions: Conserved and lineage-specific SNPs can be imputed with a high degree of accuracy from limited viral polymorphic data due to the lack of recombination and the stochastic mechanism of variation accumulation in the HPV genome. However, to determine the role of novel variants or non-lineage-specific SNPs by VWAS will require direct sequence analysis. The investigation of patterns of genetic variation and the identification of diagnostic SNPs for lineages of HPV16 variants provides a valuable resource for future studies of HPV16 pathogenicity. [ABSTRACT FROM AUTHOR]

Abstract: The Hawaiian Drosophilidae are comprised of an estimated 1000 species, all arising from a single common ancestor in the last 25 million years. This group, because of its species diversity, marked sexual dimorphism and complex mating behavior, host plant specificity, and the well-known chronology of the Hawaiian Archipelago, is an excellent model system for evolutionary studies. Here we present a phylogeny of this group based on ∼2.6kb of mitochondrial DNA sequence. Our taxon sampling is the most extensive to date, with nearly 200 species representing all species groups and most subgroups from the larger clades. Our results suggest that the picture wing and modified mouthpart species, long believed to be derived within this radiation, may actually occupy a basal position in the phylogeny. The haleakale species group, in contrast, is strongly supported as sister to the AMC clade. We use the phylogenetic results to examine the evolution of two important ecological characters, the host family and type of substrate used for oviposition and larval development. Although both host and substrate transitions are common in the group, oviposition substrate is more conserved among species groups than host plant family. While the ancestral host plant family is equivocally reconstructed, our results suggest that the ancestor of this group may have used rotting bark as a primary oviposition substrate. [Copyright &y& Elsevier]

Abstract: DNA barcoding has recently been proposed as a promising tool for the (1) rapid assignment of unknown samples to described species by non-expert workers and (2) a potential method of new species discovery based on degree of DNA sequence divergence. Two broad methods have been used, one based on degree of DNA sequence variation, within and between species and another requiring the recovery of species as discrete clades (monophyly) on a phylogenetic tree. An alternative method relies on the identification of a set of specific diagnostic nucleotides for a given species (characters). The genus Drosophila has long served as a model system in genetics, development, ecology and evolutionary biology. As a result of this work, species boundaries within this genus are quite well delimited, with most taxa being defined by morphological characters and also conforming to a biological species concept (e.g., partial or complete reproductive isolation has used to erect and define species). In addition, some of the species in this group have also been subjected to phylogenetic analysis, yielding cases where taxa both conform and conflict with a phylogenetic species concept. Here, we analyzed 1058 COI sequences belonging to 68 species belonging to Drosophila and its allied genus Zaprionus and with more than a single representative to assess the performance of the three DNA barcoding methods. 26% of the species could not be defined using distance methods, i.e. had a barcoding gap of⩽0, and 23% were not monophyletic. We focused then on four groups of closely-related species whose taxonomy is well-established on non-molecular basis (e.g., morphology, geography, reproductive isolation) and to which most of the problematic species belonged. We showed that characters performed better than other approaches in the case of paraphyletic species, but all methods failed in the case of polyphyletic species. For these polyphyletic species, other sources of evidence (e.g., morphology, geography, reproductive isolation) are more relevant than COI sequences, highlighting the limitation of DNA barcoding and the needs for integrative taxonomy approaches. In conclusion, DNA barcoding of Drosophila shows no reason to alter the 250years old tradition of character-based taxonomy, and many reasons to shy away from the alternatives. [Copyright &y& Elsevier]

Background: Genome level analyses have enhanced our view of phylogenetics in many areas of the tree of life. With the production of whole genome DNA sequences of hundreds of organisms and large-scale EST databases a large number of candidate genes for inclusion into phylogenetic analysis have become available. In this work, we exploit the burgeoning genomic data being generated for plant genomes to address one of the more important plant phylogenetic questions concerning the hierarchical relationships of the several major seed plant lineages (angiosperms, Cycadales, Gingkoales, Gnetales, and Coniferales), which continues to be a work in progress, despite numerous studies using single, few or several genes and morphology datasets. Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group. Methodology: We exploited the EST database to construct a supermatrix of DNA sequences (over 1,200 concatenated orthologous gene partitions for 17 taxa) to examine non-flowering seed plant relationships. This analysis employed programs that offer rapid and robust orthology determination of novel, short sequences from plant ESTs based on reference seed plant genomes. Our phylogenetic analysis retrieved an unbiased (with respect to gene choice), well-resolved and highly supported phylogenetic hypothesis that was robust to various outgroup combinations. Conclusions: We evaluated character support and the relative contribution of numerous variables (e.g. gene number, missing data, partitioning schemes, taxon sampling and outgroup choice) on tree topology, stability and support metrics. Our results indicate that while missing characters and order of addition of genes to an analysis do not influence branch support, inadequate taxon sampling and limited choice of outgroup(s) can lead to spurious inference of phylogeny when dealing with phylogenomic scale data sets. As expected, support and resolution increases significantly as more informative characters are added, until reaching a threshold, beyond which support metrics stabilize, and the effect of adding conflicting characters is minimized. [ABSTRACT FROM AUTHOR]

Abstract: The Hawaiian Drosophila offer a unique opportunity to examine evolutionary questions because of the known ages of the Hawaiian Islands and the large number of species endemic to this archipelago. One of the more well studied groups of Hawaiian Drosophila is the planitibia species group, a long-standing population genetic model system. Here we present a molecular phylogenetic hypothesis of all 17 taxa in the planitibia group based on nucleotide sequences from two mitochondrial (16S and COII) and four nuclear (Adh, Gpdh, Yp1, and Yp2) loci, accounting for over 4kb of sequence per taxon. We use these data to estimate major divergence times within this group. Our results suggest that the basal diversification within this group, calculated at 6.1±0.47 MY, predates the oldest high island of Kauai. The older diversifications in this group took place on Kauai, with subsequent colonization and speciation events occurring as new islands became available to Drosophila. Understanding of the phylogenetic relationships of this important group will place the existing population genetic work in a macroevolutionary context and stimulate additional work, particularly on those taxa endemic to the Maui Nui complex of islands. [Copyright &y& Elsevier]

Aggregatibacter actinomycetemcomitans is implicated in localized aggressive periodontitis. We report the first genome sequence of an A. actinomycetemcomitans strain isolated from an Old World primate. [ABSTRACT FROM AUTHOR]

Background:The species Alphapapillomavirus 7 (alpha-7) contains human papillomavirus genotypes that account for 15% of invasive cervical cancers and are disproportionately associated with adenocarcinoma of the cervix. Complete genome analyses enable identification and nomenclature of variant lineages and sublineages. Methods:The URR/E6 region was sequenced to screen for novel variants of HPV18, 39, 45, 59, 68, 70, 85 and 97 from 1147 cervical samples obtained from multiple geographic regions that had previously been shown to contain an alpha-7 HPV isolate. To study viral heterogeneity, the complete 8 kb genome of 128 isolates, including 109 sequenced for this analysis, were annotated and analyzed. Viral evolution was characterized by constructing phylogenic trees using maximum-likelihood and Bayesian algorithms. Global and pairwise alignments were used to calculate total and ORF/region nucleotide differences; lineages and sublineages were assigned using an alphanumeric system. The prototype genome was assigned to the A lineage or A1 sublineage. Results:The genomic diversity of alpha-7 HPV types ranged from 1.1% to 6.7% nucleotide sequence differences; the extent of genome-genome pairwise intratype heterogeneity was 1.1% for HPV39, 1.3% for HPV59, 1.5% for HPV45, 1.6% for HPV70, 2.1% for HPV18, and 6.7% for HPV68. ME180 (previously a subtype of HPV68) was designated as the representative genome for HPV68 sublineage C1. Each ORF/region differed in sequence diversity, from most variable to least variable: noncoding region 1 (NCR1) / noncoding region 2 (NCR2) > upstream regulatory region (URR) > E6 / E7 > E2 / L2 > E1 / L1. Conclusions:These data provide estimates of the maximum viral genomic heterogeneity of alpha-7 HPV type variants. The proposed taxonomic system facilitates the comparison of variants across epidemiological and molecular studies. Sequence diversity, geographic distribution and phylogenetic topology of this clinically important group of HPVs suggest an independent evolutionary history for each type. [ABSTRACT FROM AUTHOR]