Begonia is the world’s fastest-growing genus and a focus of intense taxonomic research. To support this, a stable and useful sectional classification is needed. This paper reviews the feasibility and challenges of creating an infrageneric classification for Begonia based on phylogenetic data, and how to overcome phylogenetic and taxonomic conflict. In particular, it (i) tests genus-wide patterns of incongruence between phylogenies based on the nuclear, chloroplast and mitochondrial genomes; (ii) explains organelle inheritance and its contribution to phylogenetic incongruence, and (iii) presents a manifesto for a workable and stable subgeneric classification in light of the above and lays the foundation for a collaborative Begonia Phylogeny Group.

Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like † Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.

The tapertail anchovy (Coilia nasus) is an economically important species, mainly distributed along the coast of the northwestern Pacific and associated freshwater bodies, including the Qiantang River, the Yangtze River, the Liaohe River, and the Yalu River of China, and further eastward to Korean Peninsula and Ariake Sound of Japan. There have been many studies on population genetics of C. nasus, but those were either focused on a few populations or used limited number of loci. The results are still controversial and the range-wide population structure of C. nasus is not resolved. This study is aimed to estimate genetic differences among populations from Japan, Korea and the major drainages of China using thousands of loci collected by exon-capture method. The reconstructed maximum likelihood tree, Network, and STRUCTURE analysis confirmed that the population from Lake Dongting should be considered as a separate species, C. brachygnathus, whereas the other populations were mixed together except that fish collected from the Shuangtaizi River of Liaohe drainage were grouped with the fish from Dongting. The AMOVA revealed that genetic variation was 6.36% among populations and 93.61% among individuals within population, when C. brachygnathus was excluded from the analysis. Pairwise FST showed that genetic difference between C. brachygnathus and C. nasus was high (0.0889–0.7350) and difference among the other populations were low (0.0086–0.3127) but significant, suggesting imperfect natal homing of migratory C. nasus. According to our results, an integrated management strategy should be taken jointly by the countries of this region to protect the valuable fisheries resource of C. nasus.

Abstract Bonytongues (Osteoglossomorpha) constitute an ancient clade of teleost fishes distributed in freshwater habitats throughout the world. The group includes well-known species such as arowanas, featherbacks, pirarucus, and the weakly electric fishes in the family Mormyridae. Their disjunct distribution, extreme morphologies, and electrolocating capabilities (Gymnarchidae and Mormyridae) have attracted much scientific interest, but a comprehensive phylogenetic framework for comparative analysis is missing, especially for the species-rich family Mormyridae. Of particular interest are disparate craniofacial morphologies among mormyrids which might constitute an exceptional model system to study convergent evolution. We present a phylogenomic analysis based on 546 exons of 179 species (out of 260), 28 out of 29 genera, and all six families of extant bonytongues. Based on a recent reassessment of the fossil record of osteoglossomorphs, we inferred dates of divergence among transcontinental clades and the major groups. The estimated ages of divergence among extant taxa (e.g., Osteoglossomorpha, Osteoglossiformes, and Mormyroidea) are older than previous reports, but most of the divergence dates obtained for clades on separate continents are too young to be explained by simple vicariance hypotheses. Biogeographic analysis of mormyrids indicates that their high species diversity in the Congo Basin is a consequence of range reductions of previously widespread ancestors and that the highest diversity of craniofacial morphologies among mormyrids originated in this basin. Special emphasis on a taxon-rich representation for mormyrids revealed pervasive misalignment between our phylogenomic results and mormyrid taxonomy due to repeated instances of convergence for extreme craniofacial morphologies. Estimation of ancestral phenotypes revealed contingent evolution of snout elongation and unique projections from the lower jaw to form the distinctive Schnauzenorgan. Synthesis of comparative analyses suggests that the remarkable craniofacial morphologies of mormyrids evolved convergently due to niche partitioning, likely enabled by interactions between their exclusive morphological and electrosensory adaptations. [Africa; ancestral state estimation; diversity; exon capture; freshwater fishes; Phylogenomics.]

Understanding patterns of diversification, genetic exchange, and pesticide resistance in arthropod disease vectors is necessary for effective population management. With the availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for a large number of genetic markers. To this end, the targeting of gene sequences of known function can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens such as avian malaria parasites that are detrimental to birds. Here we describe the development of a targeted, gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we sequenced samples from several members of the complex, as well as from distinct populations of the relatively under-studied Culex quinquefasciatus . The data generated was then used to examine taxonomic divergence and population clustering between and within these mosquitoes. We also used this data to investigate genetic variants present in our samples that had previously been shown to correlate with insecticide-resistance. Broadly, our gene capture approach successfully enriched the genomic regions of interest, and proved effective for facilitating examinations of taxonomic divergence and geographic clustering within the Cx . pipiens complex. It also allowed us to successfully survey genetic variation associated with insecticide resistance in Culex mosquitoes. This enrichment protocol will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of these ubiquitous and increasingly damaging disease vectors.

Across herbivorous insect clades, species richness and host-use diversity tend to positively covary. This could be because host-use divergence drives speciation, or because it raises the ecological limits on species richness. To evaluate these hypotheses, we performed phylogenetic path model analyses of the species diversity of Nearctic aphids. Here, we show that variation in the species richness of aphid clades is caused mainly by host-use divergence, whereas variation in speciation rates is caused more by divergence in non-host-related niche variables. Aphid speciation is affected by both the evolution of host and non-host-related niche components, but the former is largely caused by the latter. Thus, our analyses suggest that host-use divergence can both raise the ecological limits on species richness and drive speciation, although in the latter case, host-use divergence tends to be a step along the causal path leading from non-host-related niche evolution to speciation.

To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers. , A mosaic approach to protection The COVID-19 pandemic has been ongoing for more than 2 years now, and new variants such as Omicron are less susceptible to the vaccines developed against earlier lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, there is continued risk of spillovers of other animal sarbecoviruses into humans. There is thus a need for vaccines that will give broader protection. Cohen et al . developed mosaic nanoparticles that display the receptor-binding domains (RBDs) from SARS-CoV-2 and seven other animal sarbecoviruses. Mosaic nanoparticles protected against both SARS-CoV-2 and SARS-CoV challenges in animal models even though the SARS-CoV RBD was not present on the mosaic-8 RBD nanoparticles. By contrast, a homotypic SARS-CoV-2 RBD nanoparticle (presenting only SARS-CoV-2 RBDs) only protected against a SARS-CoV-2 challenge. —VV , A mosaic sarbecovirus nanoparticle protects against SARS-2 and SARS-1, whereas a SARS-2 nanoparticle only protects against SARS-2. , INTRODUCTION Two animal coronaviruses from the severe acute respiratory syndrome (SARS)–like betacoronavirus (sarbecovirus) lineage, SARS coronavirus (SARS-CoV) and SARS-CoV-2, have caused epidemics or pandemics in humans in the past 20 years. SARS-CoV-2 triggered the COVID-19 pandemic that has been ongoing for more than 2 years despite rapid development of effective vaccines. Unfortunately, new SARS-CoV-2 variants, including multiple heavily mutated Omicron variants, have prolonged the COVID-19 pandemic. In addition, the discovery of diverse sarbecoviruses in bats raises the possibility of another coronavirus pandemic. Hence, there is an urgent need to develop vaccines and therapeutics to protect against both SARS-CoV-2 variants and zoonotic sarbecoviruses with the potential to infect humans. RATIONALE To combat future SARS-CoV-2 variants and spillovers of sarbecoviruses threatening global health, we designed nanoparticles that present 60 randomly arranged spike receptor-binding domains (RBDs) derived from the spike trimers of eight different sarbecoviruses (mosaic-8 RBD nanoparticles) to elicit antibodies against conserved and relatively occluded—rather than variable, immunodominant, and exposed—epitopes. The probability of two adjacent RBDs being the same is low for mosaic-8 RBD nanoparticles, a feature chosen to favor interactions with B cells whose bivalent receptors can cross-link between adjacent RBDs to use avidity effects to favor recognition of conserved, but sterically occluded, RBD epitopes. By contrast, nanoparticles that present 60 copies of SARS-CoV-2 RBDs (homotypic RBD nanoparticles) are theoretically more likely to engage B cells with receptors that recognize immunodominant and sterically accessible, but less conserved, RBD epitopes. RESULTS We compared immune responses elicited by mosaic-8 (SARS-CoV-2 RBD plus seven animal sarbecoviruses RBDs) and homotypic (only SARS-CoV-2 RBDs) nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not represented with an RBD on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization produced antisera that showed equivalent neutralization of SARS-CoV-2 variants, including Omicron variants, and protected from both SARS-CoV-2 and SARS-CoV challenges in mice and nonhuman primates (NHPs), whereas homotypic SARS-CoV-2 immunization protected from SARS-CoV-2 challenge but not from SARS-CoV challenge in mice. Epitope mapping of polyclonal antisera by using deep mutational scanning of RBDs demonstrated targeting of conserved epitopes after immunization with mosaic-8 RBD nanoparticles, in contrast with targeting of variable epitopes after homotypic SARS-CoV-2 RBD nanoparticle immunization, which supports the hypothesized mechanism by which mosaic RBD nanoparticle immunization can overcome immunodominance effects to direct production of antibodies against conserved RBD epitopes. Given the recent plethora of SARS-CoV-2 variants that may be arising at least in part because of antibody pressure, a relevant concern is whether more conserved RBD epitopes might be subject to substitutions that would render vaccines and/or monoclonal antibodies targeting these regions ineffective. This scenario seems unlikely because RBD regions conserved between sarbecoviruses and SARS-CoV-2 variants are generally involved in contacts with other regions of spike trimer and therefore less likely to tolerate selection-induced substitutions. CONCLUSION Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers—in particular, highlighting the potential for a mosaic nanoparticle approach to elicit more broadly protective antibody responses than those with homotypic nanoparticle approaches. Mosaic RBD nanoparticle vaccination protects and elicits antibodies against conserved epitopes. Mosaic-8 elicited broader cross-reactive responses than those of homotypic nanoparticles. In a stringent infection model [K18-human angiotensin-converting enzyme 2 (K18-hACE2)], both protected against matched challenge (SARS-CoV-2 Beta), but only mosaic-8 also protected against a mismatch (SARS-CoV). Mosaic-8–immunized NHPs were protected against mismatched SARS-CoV-2 (Delta) and SARS-CoV. Mosaic-8–elicited antibodies predominantly bound conserved epitopes, whereas homotypic-elicited antibodies predominantly bound variable epitopes.