Antibody Responses to the SARS-CoV-2 Ancestral Strain and Omicron Variants in Moderna mRNA-1273 Vaccinated Active-Duty US Navy Sailors and Marines.

Omicron and its subvariants have steadily gained greater capability of immune escape compared to other variants of concern, resulting in an increased incidence of reinfections even among vaccinated individuals. We evaluated the antibody response to Omicron BA.1, BA.2, and BA.4/5 in US military members vaccinated with the primary 2-dose series of Moderna mRNA-1273 in a cross-sectional study. While nearly all vaccinated participants had sustained spike (S) IgG and neutralizing antibodies (ND50) to the ancestral strain, only 7.7% participants had detectable ND50 to Omicron BA.1 at 8 months postvaccination. The neutralizing antibody response to BA.2 and BA.5 was similarly reduced. The reduced antibody neutralization of Omicron correlated with the decreased antibody binding to the receptor-binding domain. The participants' seropositivity to the nuclear protein positively correlated with ND50. Our data emphasizes the need for continuous vigilance in monitoring for emerging variants and the need to identify potential alternative targets for vaccine design.

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution.

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

Cambrian spiral-plated echinoderms from Gondwana reveal the earliest pentaradial body plan.

Echinoderms are unique among animal phyla in having a pentaradial body plan, and their fossil record provides critical data on how this novel organization came about by revealing intermediate stages. Here, we report a spiral-plated animal from the early Cambrian of Morocco that is the most primitive pentaradial echinoderm yet discovered. It is intermediate between helicoplacoids (a bizarre group of spiral-bodied echinoderms) and crown-group pentaradiate echinoderms. By filling an important gap, this fossil reveals the common pattern that underpins the body plans of the two major echinoderm clades (pelmatozoans and eleutherozoans), showing that differential growth played an important role in their divergence. It also adds to the striking disparity of novel body plans appearing in the Cambrian explosion.

Taxonomic structure of the fossil record is shaped by sampling bias.

Understanding biases that affect how species are partitioned into higher taxa is critical for much of paleobiology, as higher taxa are commonly used to estimate species diversity through time. We test the validity of using higher taxa as a proxy for species diversity for the first time by examining one of the best fossil records we have, that of deep-sea microfossils. Using a new, taxonomically standardized, data set of coccolithophorid species and genera recorded from 143 deep-sea drilling sites in the North Atlantic, Caribbean, and Mediterranean, we show that there is a two-stepped change in the ratio of species to genera over the last 150 myr. This change is highly unexpected and correlates strongly with changes in both the number of deep-sea sites yielding coccolithophorids that have been studied and with the number of taxonomists who have published on those sections. The same pattern is present in both structurally complex heterococcoliths and the simpler nannoliths, suggesting that increasing complexity is not the driving factor. As a stepped species-to-genus ratio exists even after subsampling to standardize either the numbers of sites or numbers of papers, both factors must be contributing substantially to the observed pattern. Although some limited biological signature from major extinction events can be recognized from changes in the species-to-genus ratio, the numbers of sites and the numbers of taxonomists combined explain some 82% of the observed variation over long periods of geological time. Such a strong correlation argues against using raw species-to-genus ratios to infer biological processes without taking sampling into account and suggests that higher taxa cannot be taken as unbiased proxies for species diversity.

The diversity and biogeography of the Coleoptera of Churchill: insights from DNA barcoding.

BACKGROUND: Coleoptera is the most diverse order of insects (>300,000 described species), but its richness diminishes at increasing latitudes (e.g., ca. 7400 species recorded in Canada), particularly of phytophagous and detritivorous species. However, incomplete sampling of northern habitats and a lack of taxonomic study of some families limits our understanding of biodiversity patterns in the Coleoptera. We conducted an intensive biodiversity survey from 2006-2010 at Churchill, Manitoba, Canada in order to quantify beetle species diversity in this model region, and to prepare a barcode library of beetles for sub-arctic biodiversity and ecological research. We employed DNA barcoding to provide estimates of provisional species diversity, including for families currently lacking taxonomic expertise, and to examine the guild structure, habitat distribution, and biogeography of beetles in the Churchill region. RESULTS: We obtained DNA barcodes from 3203 specimens representing 302 species or provisional species (the latter quantitatively defined on the basis of Molecular Operational Taxonomic Units, MOTUs) in 31 families of Coleoptera. Of the 184 taxa identified to the level of a Linnaean species name, 170 (92.4%) corresponded to a single MOTU, four (2.2%) represented closely related sibling species pairs within a single MOTU, and ten (5.4%) were divided into two or more MOTUs suggestive of cryptic species. The most diverse families were the Dytiscidae (63 spp.), Staphylinidae (54 spp.), and Carabidae (52 spp.), although the accumulation curve for Staphylinidae suggests that considerable additional diversity remains to be sampled in this family. Most of the species present are predatory, with phytophagous, mycophagous, and saprophagous guilds being represented by fewer species. Most named species of Carabidae and Dytiscidae showed a significant bias toward open habitats (wet or dry). Forest habitats, particularly dry boreal forest, although limited in extent in the region, were undersampled. CONCLUSIONS: We present an updated species list for this region as well as a species-level DNA barcode reference library. This resource will facilitate future work, such as biomonitoring and the study of the ecology and distribution of larvae.

Cambrian problematica and the diversification of deuterostomes.

Vetulicolians are an enigmatic group of Cambrian organisms that have been affiliated at various times with arthropods, lobopodians, kinorhynchs and deuterostomes. New evidence on the structure of the lateral pores of vetulicolians published in BMC Biology strengthens the view that they may be total group deuterostomes, but unfortunately sheds no new light on early deuterostome evolution.

Phanerozoic marine diversity: rock record modelling provides an independent test of large-scale trends.

Sampling bias created by a heterogeneous rock record can seriously distort estimates of marine diversity and makes a direct reading of the fossil record unreliable. Here we compare two independent estimates of Phanerozoic marine diversity that explicitly take account of variation in sampling-a subsampling approach that standardizes for differences in fossil collection intensity, and a rock area modelling approach that takes account of differences in rock availability. Using the fossil records of North America and Western Europe, we demonstrate that a modelling approach applied to the combined data produces results that are significantly correlated with those derived from subsampling. This concordance between independent approaches argues strongly for the reality of the large-scale trends in diversity we identify from both approaches.

Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships.

Resolving evolutionary relationships in groups that underwent fast radiation in deep time is a problem for molecular phylogeny, as the scant phylogenetic signal that characterises short internal branches is generally swamped by more recent substitutions. We implement an approach, that maps how the support for rival phylogenies changes when analysing subsets of sites with either faster and more heterogeneous rates or slower and more homogeneous rates, to address a long-standing problem in deuterostome phylogeny - the interrelationships of the eleutherozoan echinoderm classes. We show that miRNA genes are phylogenetically uninformative as to the relationships of asteroids, echinoids and ophiuroids, consistent with a rapid radiation of these groups as suggested by their fossil record. Using three nuclear rRNAs and seven nuclear housekeeping genes, we map the support for the three possible phylogenetic arrangements of asteroids, ophiuroids and echinoids when moving between subsets of the data with very similar or very different rates of evolution. Only one of the three possible topologies (asteroids (ophiuroids+echinoids)) strengthens when the most rate-homogeneous subset of data are analysed. The other two possible pairings become stronger in a less reliable data subset, which includes the fastest and thus homoplasy-rich data in our alignment. Thus, while superficial analysis of our concatenated alignment identifies asteroids and ophiuroids as sister taxa, more thorough analyses suggest that ophiuroids may be more closely related to echinoids. Divergence of these echinoderm groups, using a relaxed molecular clock, is estimated to have occurred within ≈ 5 million years. Our results illustrate that the analytic approach of phylogenetic signal dissection can be a powerful tool to investigate rapid radiations in deep geologic time.

Modelling the past: new generation approaches to understanding biological patterns in the fossil record.

The history of life on this planet is gleaned from analysing how fossils are distributed through time and space. While these patterns are now rather securely known, at least for well-studied parts of the world, their interpretation remains far from simple. Fossils preserve only partial data from which to reconstruct their biology and the geological record is incomplete and biased, so that taxonomic ranges and palaeocommunity structure are imperfectly known. To better understand the often highly complex deep-time processes that gave rise to the empirical fossil record, palaeontologists have turned to modelling the past. Here, we summarize a series of 11 papers that showcase where modelling the past is being applied to advance our understanding across a wide spectrum of current palaeontological endeavours.

Australian Melolonthini (Coleoptera: Scarabaeidae: Melolonthinae): a third species of Allothnonius Britton, 1978, and notes on the other known species.

The genus Allothnonius Britton, 1978 (Coleoptera: Scarabaeidae: Melolonthinae: Melolonthini) is revised based on material of the two previously described Queensland species, A. barretti Britton, 1978 and A. brooksi Britton, 1978; and A. mouldsi Allsopp Smith, new species, from the northwest of the Northern Territory. The diagnostic characters of the genus are revised, distinguishing it from other Australian Melolonthini. The female of A. brooksi is described for the first time. An identification key, distribution map and notes on the natural history of the three species are included.

A review of the flightless genus Nanotermitodius Howden, 2003 (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini).

The genus Nanotermitodius Howden, 2003 (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini) is reviewed and a new species described. Only two species are presently known in the genus, Nanotermitodius andersoni Skelley, Smith, & Mora-Aguilar, new species, and Nanotermitodius peckorum Howden, 2003, which both occur in Oaxaca, Mexico. A key and distribution map for the species are presented.

Palaeoanatomy and biological affinities of a Cambrian deuterostome (Stylophora).

Stylophora are a peculiar extinct group of asymmetrical deuterostomes whose biological affinity has been fiercely debated. Disarticulated skeletal elements of a ceratocystid stylophoran recovered from the earliest Middle Cambrian of Morocco are not only the oldest stylophorans in the fossil record, but their exceptional preservation provides crucial data on the microstructure of its skeleton. Stylophoran plates are constructed of a three-dimensional mesh, termed 'stereom', identical to that of living echinoderms in which stereom microstructure provides a reliable guide to the nature of the investing soft tissues. Using modern echinoderm anatomy to interpret stereom microstructure of stylophoran elements, here we show that the large proximal lumen of their appendage was filled with muscle and that ligamentary tissues bound distal elements firmly together. We find no evidence for a mouth in the proximal lumen and no evidence that the covering plates of the appendage were articulated. Thus, although skeletal structure suggests that stylophorans are echinoderms, their appendage was not a feeding arm but a muscular locomotory organ.

Compsodactylus Fuhrmann, 2012 (Coleoptera: Scarabaeidae: Melolonthinae): distributional notes and a new species.

A new species of Compsodactylus Fuhrmann, 2012 (Coleoptera: Scarabaeidae: Melolonthinae: Macrodactylini) is described from Peru. New provincial records for Compsodactylus argentinus (Moser, 1919) are detailed for Argentina: Córdoba and Misiones. A revised key to Compsodactylus species is presented.

Liogenys Guerin-Méneville, 1831 (Coleoptera: Scarabaeidae: Melolonthinae: Diplotaxini) of northern South America and Central America: taxonomic overview with four new species.

The biodiversity of northern South American and Central American Liogenys Guérin-Méneville, 1831 (Coleoptera: Scarabaeidae: Melolonthinae: Diplotaxini) is reviewed. Four new species are described: L. clipeosetosa Cherman, new species; L. genieri Smith Cherman, new species; L. granadina Cherman, new species; and L. schneiderae Cherman, new species. The male of L. quadridens (Fabricius, 1798) and the female of L. quadridentata Blanchard, 1851 are described for the first time. Liogenys gebieni Moser, 1921 is a new junior subjective synonym of L. macropelma Bates, 1887. The northernmost record of Liogenys is emended to Trinidad and Tobago for L. granadina Cherman, new species and L. schneiderae new species. Diplotaxis puberea cuprascens (Bates, 1887) new combination, Diplotaxis puberea puberea (Bates, 1887) new combination, and Diplotaxis pubisternis (Bates, 1887) new combination are all transferred from Liogenys to Diplotaxis Kirby, 1837. Lectotypes are designated for Liogenys gebieni Moser, 1921; Melolontha quadridens Fabricius, 1798; and Liogenys quadridentatus Blanchard, 1851. An identification key to northern South American Liogenys is presented.

On the tribal classification of the Nearctic Melolonthinae (Coleoptera: Scarabaeidae), with descriptions of new species of Acoma Casey, 1889.

The subfamily Melolonthinae (Coleoptera: Scarabaeidae) is defined and characterized, and a brief summary of the world melolonthine tribes and their distributions are provided. Nearctic genera previously considered incertae sedis (Acoma Casey, 1889, Chaunocolus Saylor, 1937 and Chnaunanthus Burmeister, 1844, Phobetus LeConte, 1856, and Warwickia Smith Evans, 2005) are each placed in the proposed new tribes Acomini, Chnaunanthini, Phobetusini, and Warwickiini, respectively. Tribal assignments for all Nearctic melolonthine genera are presented. Acoma chihuahuaensis, A. eusexfoliata, A. nonglabrata, and A. pararobusta are all new species described from Mexico. The only known example of a female Acoma, represented by a specimen of A. knulli Howden, 1958, is figured and characterized. The generic composition of the Nearctic Melolonthini and Rhizotrogini is examined. Madiniella Chalumeau Gruner, 1976, previously placed in Tanyproctini, is transferred to Rhizotrogini. The subfamilies Oncerinae and Podolasiinae are each removed as tribes from the Melolonthinae and elevated to the subfamily level within Scarabaeidae. The subtribe Triodonina is placed in synonymy with the tribe Rhizotrogini. An updated generic checklist and tribal key of the Nearctic Melolonthinae are provided.

Liogenys Guérin-Méneville, 1831 (Coleoptera: Scarabaeidae: Melolonthinae) from the southern South American Transition Zone and boundaries: taxonomic overview with four new species.

The biodiversity of Liogenys Guérin-Méneville, 1831 (Coleoptera: Scarabaeidae: Melolonthinae: Diplotaxini) from the southern South American Transition Zone and boundaries is presented. Four new species are described: L. brachyclypeata Cherman, new species; L. lucialmeidae Cherman, new species; L. martinezi Cherman, new species; and L. maxillaricuspis Cherman, new species. The synonymy of L. flaveola Moser, 1924 (= L. kadleci Frey, 1970) is proposed. Lectotypes are designated for L. flavida Moser, 1918; L. pallidicornis Blanchard, 1851 (currently L. xanthocera Harold, 1869); and L. rufoflava Moser, 1918. Redescriptions are provided for all the species mentioned above plus L. calcarata Frey, 1970 and L. kunzteni Moser, 1921, as well as an identification key and updated geographical distributions to all species in the region. All species are present in the Monte province, except of L. kuntzeni (Andean provinces of Chile). Liogenys flavida and L. rufoflava have the broadest distribution, the latter here expanded to Paraguay and Chile.

DNA barcodes reveal 63 overlooked species of Canadian beetles (Insecta, Coleoptera).

This study demonstrates the power of DNA barcoding to detect overlooked and newly arrived taxa. Sixty-three species of Coleoptera representing 25 families are studied based on DNA barcode data and morphological analysis of the barcoded specimens. Three of the species involve synonymies or previous taxonomic confusion in North America, while the first Canadian records are published for 60 species. Forty-two species are adventive in North America, and 40 of these adventive species originate from the Palaearctic region. Three genera are recorded from the Nearctic region for the first time: Coelostoma Brullé, 1835 (Hydrophilidae), Scydmoraphes Reitter, 1891 (Staphylinidae), and Lythraria Bedel, 1897 (Chrysomelidae). Two new synonymies are established: Mycetoporus triangulatus Campbell, 1991 (Staphylinidae) is a junior synonym of Mycetoporus reichei Pandellé, 1869, syn. nov. while Bledius philadelphicus Fall, 1919 (Staphylinidae) is a junior synonym of Bledius gallicus (Gravenhorst, 1806), syn. nov. The previously suggested move of Ctenicera tigrina (Fall, 1901) to the genus Pseudanostirus Dolin, 1964 (Elateridae) is formalized, resulting in Pseudanostirus tigrinus (Fall, 1901), comb. nov.

Deuterostomes in a twist: the origins of a radical new body plan.

Echinoderms have a unique ontogeny and adult structure, and, among Bilateria, are the phylum that has diverged most radically in appearance from the ancestral body plan. Embryology and gene expression studies suggest how this transformation may have occurred while paleontological data provide direct evidence for the order in which these events took place. Comparing echinoderm ontogeny and genetic developmental signalling patterns with those of their sister group, the hemichordates, suggests that an evolutionary switch from posterior facultative to anterior obligate larval attachment proved the critical trigger. This necessitated introduction of a phase of torsion in development to bring the mouth into a more appropriate orientation for filter feeding, which in turn rotated the axis of the developing adult 90 degrees out of alignment with Hox and other body patterning genes. As a result the developing echinoderm rudiment came to receive a complex mosaic of anterior-posterior signalling, and extensive co-option of signalling pathways was able to take place. The fossil record shows that early (pre-radiate) echinoderms were much more hemichordate-like, with a muscular post-anal stalk and facultative attachment, and probably developed maintaining continuity with larval axes, as in hemichordates, although left-right asymmetry was more highly developed. Anterior attachment and torsion, however, were clearly part of the developmental pattern of helicoplacoids and (to a much greater extent) in subsequent pentaradiate forms.

A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site.

DNA gyrase is the only topoisomerase able to introduce negative supercoils into DNA. Absent in humans, gyrase is a successful target for antibacterial drugs. However, increasing drug resistance is a serious problem and new agents are urgently needed. The naturally-produced Escherichia coli toxin CcdB has been shown to target gyrase by what is predicted to be a novel mechanism. CcdB has been previously shown to stabilize the gyrase 'cleavage complex', but it has not been shown to inhibit the catalytic reactions of gyrase. We present data showing that CcdB does indeed inhibit the catalytic reactions of gyrase by stabilization of the cleavage complex and that the GyrA C-terminal DNA-wrapping domain and the GyrB N-terminal ATPase domain are dispensable for CcdB's action. We further investigate the role of specific GyrA residues in the action of CcdB by site-directed mutagenesis; these data corroborate a model for CcdB action based on a recent crystal structure of a CcdB-GyrA fragment complex. From this work, we are now able to present a model for CcdB action that explains all previous observations relating to CcdB-gyrase interaction. CcdB action requires a conformation of gyrase that is only revealed when DNA strand passage is taking place.

Taxonomic review of Athliini (Coleoptera: Scarabaeidae: Melolonthinae), a new tribe of scarab beetles endemic to South America.

Athliini Smith Evans, new tribe (Coleoptera: Scarabaeidae: Melolonthinae) includes four genera that occur from southern South America through to the southeastern regions of Brazil: Apteroathlia Smith Evans, new genus, Athlia Erichson, 1835, Dihymenonyx Gutiérrez, 1949, and Ulata Saylor, 1945. Justifications are provided for the new tribe and for the placement each genus in the new tribe. Keys to genera and species are presented along with distributional data and maps for all species. Apteroathlia translucida Smith Evans, new species and Apteroathlia nox Smith Evans, new species are described. Lectotypes are designated for Athlia bruchi Moser, 1924 and Athlia rustica Erichson, 1835. A neotype is designated for Ulata argentina Saylor, 1945.