Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families

Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred ‘ghost lineages’ from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate.

Identification and genetic diversity of hepatitis E virus in domestic swine from Slovakia

Background Hepatitis E virus (HEV) is agent causing hepatitis worldwide. Originally considered to be limited to developing countries, this virus was also detected in developed countries. In recent years an increasing number of reports indicate that farmed domestic pigs are widely infected with HEV in several European countries. The HEV status in Slovakia is still missing. Results In this study, the circulation of HEV among domestic swine in Slovakia and genetic diversity of the virus was studied. Overall HEV RNA was detected in 53/388 (13.7, 95% CI: 10.40–17.48%) pig rectal swabs in five production stages (age categories) with statistically significant differences among all the stages. The highest HEV prevalence was observed in weaners 24/81 (29.6, 95% CI: 19.99–40.81%) and then significantly declined in growers and fatteners. No HEV was detected in suckling piglets and sows. Twenty-eight partial sequences of ORF1 (242 bp) and seventeen of ORF2 (304 bp) were analysed. Phylogenetic analysis and p-distance comparisons confirmed in both ORFs that all Slovak HEV sequences belong to the genotype HEV-3, major clade 3abchij with higher identity to 3a and 3i subtypes. Three sequences were outside of all lastly updated HEV-3 subtypes. Conclusion This is the first report to fill the information gap about HEV infection in pigs in Slovakia. The results suggested a lower prevalence of HEV in Slovak pig farms than observed in other European countries. While most HEV isolates were typed as HEV-3 clade 3abchij, three sequences were unclassified.

Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveal similar localization, but less homology of protein sequences than expected for Nematoda phylum

Major sperm proteins (MSP) are a nematode-specific system of motor proteins required for amoeboid sperm movement. A number of MSP genes vary in different nematode species, but encoded protein sequences reveal high homology between these proteins. In fact, all studies of MSPs localization and functions are based exclusively on the representatives of the order Rhabditida belonging to the nematode class Chromadorea, while MSP-driven sperm movement in Enoplea, another major clade of the phylum Nematoda is still unconfirmed. In this study, we found out the presence of MSPs in the enoplean nematode Enoplus brevis (Enoplida) and compared MSP localization in sperm of this species with the chromadorean nematode Panagrellus redivivus (Rhabditida). Then, we analyzed the putative MSP sequences of both species. Our results indicate that MSPs are presented in E. brevis spermatozoa and form filamentous structures after sperm activation, which may be considered as the evidence of their motor functions similar to those in the spermatozoa of chromadorean nematodes. We found that E. brevis MSPs show lower homology to known proteins of rhabditids which species reveal hyper-conservatism in MSP protein sequences. It reflects evidently more distant evolutionary relationships of Enoplea and Chromadorea than exist within Rhabditida order. Our data denote necessity of reconsideration of view on MSP evolution within Nematoda.

Antibiotic treatment regimes as a driver of the global population dynamics of a major gonorrhea lineage

The Neisseria gonorrhoeae multilocus sequence type (ST) 1901 is among the lineages most commonly associated with treatment failure. Here we analyze a global collection of ST-1901 genomes to shed light on the emergence and spread of alleles associated with reduced susceptibility to extended-spectrum cephalosporins (ESCs). The genetic diversity of ST-1901 falls into a minor and a major clade, both of which were inferred to have originated in East Asia. The dispersal of the major clade from Asia happened in two separate waves expanding from around 1987 and 1996, respectively. Both waves first reached North America, and from there spread to Europe and Oceania, with multiple secondary reintroductions to Asia. The ancestor of the second wave acquired the penA 34.001 allele, which significantly reduces susceptibility to extended-spectrum cephalosporins (ESCs). Our results suggest that the acquisition of this allele granted the second wave a fitness advantage at a time when ESCs became the key drug class used to treat gonorrhea. Following its establishment globally, the lineage has served as a reservoir for the repeated emergence of clones fully resistant to the ESC ceftriaxone, an essential drug for effective treatment of gonorrhea. We infer that the effective population sizes of both clades went into decline as treatment schemes shifted from fluoroquinolones via ESC monotherapy to dual therapy with ceftriaxone and azithromycin in Europe and the USA. Despite the inferred recent population size decline, the short evolutionary path from the penA 34.001 allele to alleles providing full ceftriaxone resistance is a cause of concern.

A Molecular Survey and Genetic Diversity of Hepatitis E Virus in Domestic Swine From Slovakia

Background: Hepatitis E virus (HEV) is agent causing hepatitis worldwide. Originally considered to be limited to developing countries, this virus was also detected in developed countries. In recent years an increasing number of reports indicate that farmed domestic pigs are widely infected with HEV in several European countries including neighbouring countries the Czech Republic and Hungary. The HEV status in Slovakia is still missing.Results: In this study, the circulation of HEV among domestic swine in Slovakia and genetic diversity of the virus was studied. Overall HEV RNA was detected in 53/388 (13.7%) pig rectal swabs in five production stages (age categories) with statistically highly significant differences (P < 0.01, χ2=28.444). No HEV was detected in suckling piglets and sows. The highest HEV incidence (29.6%) was observed in weaners and then declined in growers and fatteners. Twenty-eight partial sequences of ORF1 (242 bp) and seventeen of ORF2 (304 bp) were genetically analysed. Phylogenetic analysis and p-distance comparisons confirmed in both ORFs that all Slovak HEV sequences belong to the genotype HEV-3, major clade 3abchij with higher identity to 3a and 3i subtypes. Three sequences created a new branch, outside of major clades 3abchij and 3efg, showing high nucleotide p-distances (0.140-0.178). They could represent a novel subtype.Conclusion: This is the first report to fill the epidemiological gap about HEV infection in pigs in Slovakia. The results indicated a lower incidence of HEV in Slovak pig farms than observed in other European countries. While most HEV isolates were typed as HEV-3 clade3abchij, three sequences were most probably a candidate for a new HEV-3 subtype.

Mutational landscape and dominant lineages in the SARS-CoV-2 infections in the state of Telangana, India

The novel Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) causing COVID-19 has rapidly turned into a pandemic, infecting millions and causing ~7 million deaths across the globe. In addition to studying the mode of transmission and evasion of host immune system, analysing the viral mutational landscape constitutes an area under active research. The latter is expected to impart knowledge on the emergence of different clades, subclades, viral protein functions and protein-protein and protein-RNA interactions during replication/transcription cycle of virus and response to host immune checkpoints. In this study we have attempted to bring forth the viral genomic variants defining the major clade(s) as identified from samples collected from the state of Telangana, India.

A synoptic revision of Pohliella (Podostemaceae) with notes on Aulea, Cipoia and Saxicolella

ABSTRACTSaxicolella Engl., an African genus of the waterfall specialist plant family Podostemaceae, was shown to be polyphyletic as currently delimited. One clade, sampled from species in Ghana, is sister to American Ceratolacis (Tul.)Wedd., Podostemum Michx. and all Old World Podostemoideae (podostemoids). The second clade, sampled from Cameroonian material, was embedded within the major clade of African podostemoids. In this paper the generic nomenclature applied to Saxicolella sensu lato (Saxicolella, Pohliella Engl., Aulea Lebrun & Stork nom. inval.), is reviewed and the morphological support for the two clades and their correct generic names is determined. Pohliella is shown to be the correct name for the first clade (based on Pohliella laciniata Engl., Cameroon) and a synoptic treatment of its three published species is given, one of which is extinct, and two are threatened. However, a fourth, unpublished species exists. The new combinations Pohliella submersa (J.B.Hall) Cheek and Pohliella amicorum (J.B. Hall) Cheek are made for the two published Ghanaian species. The recently described New World genus Cipoia C.T. Philbrick, Novelo & Irgang is revealed as being morphologically identical to Pohliella, but in view of the geographical disjunction, confirmation from molecular evidence is awaited before its two species are also transferred to Pohliella. The correct name for the second clade, embedded in African podostemoids, is Saxicolella (sensu stricto), now with two known species, Saxicolella nana Engl. (type of Saxicolella, Cameroon) and Saxicolella flabellata (G.Taylor) C. Cusset (Nigeria).

The iron-responsive genome of the chiton Acanthopleura granulata

ABSTRACTMolluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many biomineralization genes identified previously in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.SIGNIFICANCE STATEMENTChitons are molluscs that make shell plates, spine- or scale-like sclerites, and iron-coated teeth. Currently, all molluscs with sequenced genomes lie within one major clade (Conchifera). Sequencing the genome of a representative from the other major clade (Aculifera) helps us learn about the origins and evolution of molluscan traits. The genome of the West Indian Fuzzy Chiton, Acanthopleura granulata, reveals chitons have homologs of many genes other molluscs use to make shells, suggesting all molluscs share some shell-making pathways. The genome of A. granulata has more genes that may be regulated directly by iron than other molluscs, and chitons produce a unique isoform of a major iron-transport protein (ferritin), suggesting that chitons have genomic specializations that contribute to their production of iron-coated teeth.

Introductions and early spread of SARS-CoV-2 in France

Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections.

A new plesiosaurian from the Jurassic–Cretaceous transitional interval of the Slottsmøya Member (Volgian), with insights into the cranial anatomy of cryptoclidids using computed tomography

Cryptoclidids are a major clade of plesiosauromorph plesiosaurians best known from the Middle—Late Jurassic, but little is known regarding their turnover into the Early Cretaceous. Of the known cryptoclidid genera, most preserve only a limited amount of cranial material and of these Cryptoclidus eurymerus, displays the most complete, but compressed cranium. Thus, the lack of knowledge of the cranial anatomy of this group may hinder the understanding of phylogenetic interrelationships, which are currently predominantly based on postcranial data. Here we present a nearly complete adult cryptoclidid specimen (PMO 224.248) representing a new genus and species Ophthalmothule cryostea gen et sp. nov., from the latest Jurassic to earliest Cretaceous part of the Slottsmøya Member, of central Spitsbergen. The holotype material preserves a complete cranium, partial mandible, complete and articulated cervical, pectoral and anterior to middle dorsal series, along with the pectoral girdle and anterior humeri. High resolution microcomputed tomography reveals new data on the cranial anatomy of this cryptoclidid, including new internal features of the braincase and palate that are observed in other cryptoclidids. A phylogenetic analysis incorporating new characters reveals a novel tree topology for Cryptoclididae and particularly within the subfamily Colymbosaurinae. These results show that at least two cryptoclidid lineages were present in the Boreal Region during the latest Jurassic at middle to high latitudes.