Explore the vast range of titles available.

Eight years after DNA barcoding was formally proposed on a large scale, COI sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a COI data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1% sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from > 7% for samples within 1 km, to < 3.5% for samples up to > 6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query identifications considered uncertain (more than one species < 1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95% of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives— smaller geographical scales deliver higher accuracy.

Nomenclatural rule changes in the International Code of Nomenclature for algae, fungi and plants, adopted at the 18th International Botanical Congress in Melbourne, Australia, in 2011, provide for a single name to be used for each fungal species. The anamorphs of Epichloë species have been classified in genus Neotyphodium, the form genus that also includes most asexual Epichloë descendants. A nomenclatural realignment of this monophyletic group into one genus would enhance a broader understanding of the relationships and common features of these grass endophytes. Based on the principle of priority of publication we propose to classify all members of this clade in the genus Epichloë. We have reexamined classification of several described Epichloë and Neotyphodium species and varieties and propose new combinations and states. In this treatment we have accepted 43 unique taxa in Epichloë, including distinct species, subspecies, and varieties. We exclude from Epichloë the two taxa Neotyphodium starrii, as nomen dubium, and Neotyphodium chilense, as an unrelated taxon.

This study presents an evaluation of the currently accepted sectional classification of the genus Anthurium Schott (Araceae) in light of a recently published molecular phylogeny for the group. In general, disagreements between these two occur because many diagnostic morphological characters used in the sectional classification turned out to be highly homoplasious within Anthurium, with multiple independent gains or losses of seemingly similar morphologies in distantly related clades. A new sectional classification of Anthurium that more accurately represents species relationships and the evolutionary history of the genus is much needed, and here we propose the first steps toward it. Results from this study suggest that out of the 18 sections and two series recognized in Anthurium, only seven of these groups are monophyletic (i.e., sections Andiphilum (Schott) Croat, Calomystrium (Schott) Engl., Dactylophyllium (Schott) Engl., Leptanthurium (Schott) Engl., Polyphyllium Engl., Tetraspermium (Schott) Engl., and the newly recognized section Multinervia (Croat) Carlsen & Croat, previously a series within section Pachyneurium (Schott) Engl.). All other sections are either not monophyletic or their monophyly could not be accurately tested. A complete revision of the sectional classification of Anthurium will require a more comprehensive taxon sampling and a better supported molecular phylogeny.

Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is a member of orthopoxvirus genus. The reemergence of MPXV in 2017 (at Bayelsa state) after 39 years of no reported case in Nigeria, and the export of travelers’ monkeypox (MPX) from Nigeria to other parts of the world, in 2018 and 2019, respectively, have raised concern that MPXV may have emerged to occupy the ecological and immunological niche vacated by smallpox virus. This review X-rays the current state of knowledge pertaining the infection biology, epidemiology, and evolution of MPXV in Nigeria and worldwide, especially with regard to the human, cellular, and viral factors that modulate the virus transmission dynamics, infection, and its maintenance in nature. This paper also elucidates the role of recombination, gene loss and gene gain in MPXV evolution, chronicles the role of signaling in MPXV infection, and reviews the current therapeutic options available for the treatment and prevention of MPX. Additionally, genome-wide phylogenetic analysis was undertaken, and we show that MPXV isolates from recent 2017 outbreak in Nigeria were monophyletic with the isolate exported to Israel from Nigeria but do not share the most recent common ancestor with isolates obtained from earlier outbreaks, in 1971 and 1978, respectively. Finally, the review highlighted gaps in knowledge particularly the non-identification of a definitive reservoir host animal for MPXV and proposed future research endeavors to address the unresolved questions.

Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in February 2019. Of note, in addition to seven new virus families, the ICTV has approved, by an absolute majority, the creation of the realm Riboviria, a likely monophyletic group encompassing all viruses with positive-strand, negative-strand and double-strand genomic RNA that use cognate RNA-directed RNA polymerases for replication.

Rutaceae is a family of angiosperms well known for the economically important genus Citrus. The division of Rutaceae into subfamilies is still inadequate and provisional. Previous phylogenetic studies at the family level are characterized by a limited sampling of genera and lack several crucial taxa. Here, we present a phylogenetic study based on six nuclear and plastid markers including 87.7% of the currently accepted genera, which is more than twice as many as in previous studies. Seven genera are included in a phylogenetic analysis for the first time. Most clades are resolved with high support, and we propose a new subfamily classification for Rutaceae that comprises the subfamilies Amyridoideae, Aurantioideae, Cneoroideae, Haplophylloideae, Rutoideae and Zanthoxyloideae. Aurantioideae is the only traditional subfamily that is resolved as monophyletic. We tested whether 13 morphological and karyological characters are taxonomically informative in Rutaceae. Chromosome numbers are clearly different in the two main clades of Rutaceae, but fruit characteristics, which have been used to define subfamilies in the past, do not distinguish between the main lineages of the family.

The family Pteromalidae (Hymenoptera: Chalcidoidea) is reviewed with the goal of providing nomenclatural changes and morphological diagnoses in preparation for a new molecular phylogeny and a book on world fauna that will contain keys to identification. Most subfamilies and some tribes of Pteromalidae are elevated to family level or transferred elsewhere in the superfamily. The resulting classification is a compromise, with the aim of preserving the validity and diagnosability of other, well-established families of Chalcidoidea. The following former subfamilies and tribes of Pteromalidae are elevated to family rank: Boucekiidae, Ceidae, Cerocephalidae, Chalcedectidae, Cleonymidae, Coelocybidae, Diparidae, Epichrysomallidae, Eunotidae, Herbertiidae, Hetreulophidae, Heydeniidae, Idioporidae, Lyciscidae, Macromesidae, Melanosomellidae, Moranilidae, Neodiparidae, Ooderidae, Pelecinellidae (senior synonym of Leptofoeninae), Pirenidae, Spalangiidae, and Systasidae. The following subfamilies are transferred from Pteromalidae: Chromeurytominae and Keiraninae to Megastigmidae, Elatoidinae to Neodiparidae, Nefoeninae to Pelecinellidae, and Erotolepsiinae to Spalangiidae. The subfamily Sycophaginae is transferred to Pteromalidae. The formerly incertae sedis tribe Lieparini is abolished and its single genus Liepara is transferred to Coelocybidae. The former tribe Tomocerodini is transferred to Moranilidae and elevated to subfamily status. The former synonym Tridyminae (Pirenidae) is treated as valid. The following former Pteromalidae are removed from the family and, due to phylogenetic uncertainty, placed as incertae sedis subfamilies or genera within Chalcidoidea: Austrosystasinae, Ditropinotellinae, Keryinae, Louriciinae, Micradelinae, Parasaphodinae, Rivasia , and Storeyinae. Within the remaining Pteromalidae, Miscogastrinae and Ormocerinae are confirmed as separate from Pteromalinae, the former tribe Trigonoderini is elevated to subfamily status, the former synonym Pachyneurinae is recognized as a distinct subfamily, and as the senior synonym of Austroterobiinae. The tribe Termolampini is synonymized under Pteromalini, and the tribe Uzkini is synonymized under Colotrechnini. Most former Otitesellinae, Sycoecinae, and Sycoryctinae are retained in the tribe Otitesellini, which is transferred to Pteromalinae, and all other genera of Pteromalinae are treated as Pteromalini. Eriaporidae is synonymized with Pirenidae, with Eriaporinae and Euryischiinae retained as subfamilies. Other nomenclatural acts performed here outside of Pteromalidae are as follows: Calesidae: elevation to family rank. Eulophidae: transfer of Boucekelimini and Platytetracampini to Opheliminae, and abolishment of the tribes Elasmini and Gyrolasomyiini. Baeomorphidae is recognized as the senior synonym of Rotoitidae. Khutelchalcididae is formally excluded from Chalcidoidea and placed as incertae sedis within Apocrita. Metapelmatidae and Neanastatidae are removed from Eupelmidae and treated as distinct families. Eopelma is removed from Eupelmidae and treated as an incertae sedis genus in Chalcidoidea. The following subfamilies and tribes are described as new: Cecidellinae (in Pirenidae), Enoggerinae ( incertae sedis in Chalcidoidea), Erixestinae (in Pteromalidae), Eusandalinae (in Eupelmidae), Neapterolelapinae ( incertae sedis in Chalcidoidea), Solenurinae (in Lyciscidae), Trisecodinae (in Systasidae), Diconocarini (in Pteromalidae: Miscogastrinae), and Trigonoderopsini (in Pteromalidae: Colotrechninae). A complete generic classification for discussed taxa is provided.

Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Results Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Conclusions Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

Background The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. Results We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. Conclusions We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.