The spatiotemporal origin of Polynesian blueberries (Vaccinium).

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city in China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome, especially in the viral spike protein region, has resulted in the evolution of multiple variants and sub-variants which gives the virus the benefit of host immune evasion and thus renders modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 832 complete genomes of SARS-CoV-2 variants from the cities of Taiyuan and Wuhan in China was genetically characterized and their phylogenetic and evolutionary dynamics studied using phylogenetics, genetic similarity, and phylogenetic network analyses. This study shows that the four most prevalent lineages in Taiyuan and Wuhan are as follows: the Omicron lineages EG.5.1.1, followed by HK.3, FY.3, and XBB.1.16 (Pangolin classification), and clades 23F (EG.5.1), followed by 23H (HK.3), 22F (XBB), and 23D (XBB.1.9) (Nextclade classification), and lineage B followed by the Omicron FY.3, lineage A, and Omicron FL.2.3 (Pangolin classification), and the clades 19A, followed by 22F (XBB), 23F (EG.5.1), and 23H (HK.3) (Nextclade classification), respectively. Furthermore, our genetic similarity analysis show that the SARS-CoV-2 clade 19A-B.4 from Wuhan (name starting with 412981) has the least genetic similarity of about 95.5% in the spike region of the genome as compared to the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234), followed by the Omicron FR.1.4 from Taiyuan (name starting with 18495199) with ~97.2% similarity and Omicron DY.3 (name starting with 17485740) with ~97.9% similarity. The rest of the variants showed ≥98% similarity with the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234). In addition, our recombination analysis results show that the SARS-CoV-2 variants have three statistically significant recombinant events which could have possibly resulted in the emergence of Omicron XBB.1.16 (recombination event 3), FY.3 (recombination event 5), and FL.2.4 (recombination event 7), suggesting some very important information regarding viral evolution. Also, our phylogenetic tree and network analyses show that there are a total of 14 clusters and more than 10,000 mutations which may have probably resulted in the emergence of cluster-I, followed by 47 mutations resulting in the emergence of cluster-II and so on. The clustering of the viral variants of both cities reveals significant information regarding the phylodynamics of the virus among them. The results of our temporal phylogenetic analysis suggest that the variants of Taiyuan have likely emerged as independent variants separate from the variants of Wuhan. This study, to the best of our knowledge, is the first ever genetic comparative study between Taiyuan and Wuhan cities in China. This study will help us better understand the virus and cope with the emergence and spread of new variants at a local as well as an international level, and keep the public health authorities informed for them to make better decisions in designing new viral vaccines and therapeutics. It will also help the outbreak investigators to better examine any future outbreak.

Coronavirus disease 2019 (COVID-19) has attracted research interests from all fields. Phylogenetic and social network analyses based on connectivity between either COVID-19 patients or geographic regions and similarity between syndrome coronavirus 2 (SARS-CoV-2) sequences provide unique angles to answer public health and pharmaco-biological questions such as relationships between various SARS-CoV-2 mutants, the transmission pathways in a community and the effectiveness of prevention policies. This paper serves as a systematic review of current phylogenetic and social network analyses with applications in COVID-19 research. Challenges in current phylogenetic network analysis on SARS-CoV-2 such as unreliable inferences, sampling bias and batch effects are discussed as well as potential solutions. Social network analysis combined with epidemiology models helps to identify key transmission characteristics and measure the effectiveness of prevention and control strategies. Finally, future new directions of network analysis motivated by COVID-19 data are summarized.

The Macaronesian species of Euphorbia sect. Aphyllis subsect. Macaronesicae are distributed in four of the five archipelagos of Macaronesia and two mainland enclaves in Portugal and Morocco. The aims of this study are to investigate the biogeographic history of this group with AFLP and cpDNA markers, and to identify taxonomic entities within subsect. Macaronesicae based on genetic data, characterize them morphologically and infer the evolution of their diagnostic characters based on the reconstruction of ancestral character states. A continuous spatial diffusion analysis of AFLP data implicated Tenerife (central Canary Islands) as the area of origin of the group, followed by colonization of other Canarian islands and other Macaronesian archipelagos. Two dispersal events back to the mainland were also inferred. Our phylogenetic network, neighbour‐joining clustering and Structure analyses of AFLP data demonstrated that species are genetically well delimited and suggested that they may have originated from a combination of allopatric speciation at broad scales (among islands) and fine scales (within islands), or possibly sympatric ecological speciation followed by more recent inter‐island dispersal events. Ancestral character state reconstructions of morphological characters suggested that the ancestor of subsect. Macaronesicae was adapted to arid or mesic habitats, and traits associated with adaptation to humid habitats were acquired later. The central Canary Islands harbour the highest species diversity of this group in the Archipelago, and the highest nuclear and plastid genetic diversity. With regards to taxonomy, phylogenetic analyses and neighbour‐joining clustering analyses based on AFLPs showed two clearly differentiated genetic groups, sister to each other, which correspond to the E. atropurpurea and E. lamarckii complexes formerly recognised based on morphology. Euphorbia aphylla is recovered as sister to the rest of the species, supporting its exclusion from the two complexes. Euphorbia tuckeyana is excluded from the E. lamarckii complex.

HIV-1 Transmission Networks in a Small World

To determine the genetic and epidemiological relationship of infectious bronchitis virus (IBV) isolates from commercial poultry to attenuated live IBV vaccines we conducted a phylogenetic network analysis on the full-length S1 sequence for Arkansas (Ark), Massachusetts (Mass) and Delmarva/1639 (DMV/1639) type viruses isolated in 2015 from clinical cases by 3 different diagnostic laboratories. Phylogenetic network analysis of Ark isolates showed two predominant groups linked by 2 mutations, consistent with subpopulations found in commercial vaccines for this IBV type. In addition, a number of satellite groups surrounding the two predominant populations were observed for the Ark type virus, which is likely due to mutations associated with the nature of this vaccine to persist in flocks. The phylogenetic network analysis of Mass-type viruses shows two groupings corresponding to different manufacturers vaccine sequences. No satellite groups were observed for Mass-type viruses, which is consistent with no persistence of this vaccine type in the field. At the time of collection, no vaccine was being used for the DMV/1639 type viruses and phylogenetic network analysis showed a dispersed network suggesting no clear change in genetic distribution. Selection pressure analysis showed that the DMV/1639 and Mass-type strains were evolving under negative selection, whereas the Ark type viruses had evolved under positive selection. This data supports the hypothesis that live attenuated vaccine usage does play a role in the genetic profile of similar IB viruses in the field and phylogenetic network analysis can be used to identify vaccine and vaccine origin isolates, which is important for our understanding of the role live vaccines play in the evolutionary trajectory of those viruses.

HIV Phylogeographic Analyses and Their Application in Prevention and Early Detection Programmes: The Case of the Tijuana–San Diego Border Region

Decision letter: Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

Editor's evaluation: Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

Wockia, one of the six genera within the lepidopteran family Urodidae, currently includes nine species distributed in Holarctic, Oriental, and Neotropical regions. A new species of the genus, W. magna sp. nov., is described from Japan and South Korea. This is the first record of Urodidae from Japan. A cladistic analysis was constructed based on 27 morphological characters from five ingroup species and two outgroup taxa. A single most parsimonious tree was found (length = 38, CI = 71, RI = 70). The resulting tree failed to recover the monophyly of Wockia chewbacca and a clade Wockia sensu stricto, including four congeners from North America, temperate East Asia and Southeast Asia. Wockia sensu stricto was resolved as monophyletic and was divided into two subgroups, one including W. asperipunctella and W. magna, and the other including W. koreana and W. variata. The sister-group relationship of W. asperipunctella and W. magna was moderately supported. Synapomorphies of Wockia sensu stricto are provided from the resulting phylogeny. Systematic definitions of Wockia and other allied genera are revised. Optimal ancestral area reconstruction implemented in DIVA resulted in different hypotheses for Wockia, depending on how to constrain the maximum number of areas. The maximum area number set as two yielded a more likely scenario suggesting that Wockia sensu stricto originated in temperate East Asia and then dispersed into the Oriental region, North America, and Europe. A working hypothesis and other equally possible alternative explanations for the biogeography of Wockia are provided.

The subfamily Uromastycinae within the Agamidae is comprised of 18 species: three within the genus Saara and 15 within Uromastyx. Uromastyx is distributed in the desert areas of North Africa and across the Arabian Peninsula towards Iran. The systematics of this genus has been previously revised, although incomplete taxonomic sampling or weakly supported topologies resulted in inconclusive relationships. Biogeographic assessments of Uromastycinae mostly agree on the direction of dispersal from Asia to Africa, although the timeframe of the cladogenesis events has never been fully explored. In this study, we analysed 129 Uromastyx specimens from across the entire distribution range of the genus. We included all but one of the recognized taxa of the genus and sequenced them for three mitochondrial and three nuclear markers. This enabled us to obtain a comprehensive multilocus time‐calibrated phylogeny of the genus, using the concatenated data and species trees. We also applied coalescent‐based species delimitation methods, phylogenetic network analyses and model‐testing approaches to biogeographic inferences. Our results revealed Uromastyx as a monophyletic genus comprised of five groups and 14 independently evolving lineages, corresponding to the 14 currently recognized species sampled. The onset of Uromastyx diversification is estimated to have occurred in south‐west Asia during the Middle Miocene with a later radiation in North Africa. During its Saharo‐Arabian colonization, Uromastyx underwent multiple vicariance and dispersal events, hypothesized to be derived from tectonic movements and habitat fragmentation due to the active continental separation of Arabia from Africa and the expansion and contraction of arid areas in the region.

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

The taxonomic richness of seed plants at different taxonomic levels was compared between temperate East Asia and North America at both continental and semi-continental scales. In each comparison, land area and latitude range were adjusted to a comparable level between the two continental regions. East Asia is significantly more diverse than North America. In general, differences in taxonomic diversity arise at and below the genus level. At the continental scale, East Asia has 1.3 and 1.5 times as many genera and species, respectively, as North America. The northern part of East Asia has 1.1 times as many species as the northern part of North America. At the genus level, the northern part of East Asia is less diverse than the northern part of North America by a factor of 0.94. This pattern indicates that the diversity bias between the two continental regions results from the flora of southern East Asia. The diversity differences between East Asia and North America are not homogenously distributed across different plant groups. At the species level, East Asia had significantly more species than expected in magnoliids, alismatids, Liliidae, ranunculids, and rosids and had significantly less species in the Commelinidae, Caryophyllidae, and euasterids than North America.

ABSTRACTVibrio parahaemolyticus, a widespread marine bacterium, is responsible for a variety of diseases in marine organisms. Consumption of raw or undercooked seafood contaminated with V. parahaemolyticus is also known to cause acute gastroenteritis in humans. While numerous dsDNA vibriophages have been isolated so far, there have been few studies of vibriophages belonging to the ssDNA Microviridae family. In this study, a novel ssDNA phage, vB_VpaM_PG19 infecting V. parahaemolyticus, with a 5,572 bp ssDNA genome with a G+C content of 41.31% and encoded eight open reading frames, was isolated. Genome-wide phylogenetic analysis of the total phage isolates in the GenBank database revealed that vB_VpaM_PG19 was only related to the recently deposited vibriophage vB_VpP_WS1. The genome-wide average nucleotide homology of the two phages was 89.67%. The phylogenetic tree and network analysis showed that vB_VpaM_PG19 was different from other members of the Microviridae family and might represent a novel viral genus, together with vibriophage vB_VpP_WS1, named Vimicrovirus. One-step growth curves showed that vB_VpaM_PG19 has a short incubation period, suggesting its potential as an antimicrobial agent for pathogenic V. parahaemolyticus.IMPORTANCE Vibriophage vB_VpaM_PG19 was distant from other isolated microviruses in the phylogenetic tree and network analysis and represents a novel microviral genus, named Vimicrovirus. Our report describes the genomic and phylogenetic features of vB_VpaM_PG19 and provides a potential antimicrobial candidate for pathogenic V. parahaemolyticus.

Eastward colonization of the Mediterranean Basin by two geographically structured clades: The case of Odontites Ludw. (Orobanchaceae)

AimThe genetic diversity and distribution of earthworm species in the Mediterranean Basin has been influenced by their low vagility, as well as by the basin's complex geological and climatic history. Within this context, our objective was to evaluate the evolutionary history of hormogastrid earthworms by exploring their phylogeny, reconstructing ancestral areas and identifying potential vicariance and dispersal events.LocationWestern Mediterranean region, encompassing the geographical range of the family Hormogastridae (four genera, 30 species and subspecies).MethodsWe sampled the easternmost area of the hormogastrid range and integrated 606 new sequences with all the molecular data available from previous studies on the westernmost area. Mitochondrial and nuclear markers were amplified and sequenced, and the hormogastrid phylogeny (using Bayesian and likelihood methods) and networks were investigated. Ancestral‐area reconstructions were implemented inrasp.ResultsAncestral‐area reconstructions provided similar results for alternative phylogenetic hypotheses, placing the origin of Hormogastridae between southern France and the north‐eastern Iberian Peninsula, and highlighting north–central Sardinia as a key ancestral area for diversification of eastern Hormogastridae (Hormogaster rediiandH. samnitica). Multiple vicariance and dispersal events were detected, indicating a complex evolutionary history. Sardinian populations ofH. samniticaandH. rediiwere not monophyletic but were related to populations from other areas, suggesting that Sardinia is a more complex biogeographical region than anticipated. Our results identified a phylogenetic relationship between the southern Sardinian fauna and that of Sicily, as well as relationships between the fauna of north‐eastern Sardinia and those of the Italian Peninsula and the Tuscan Archipelago.Main conclusionsOur results suggest a complex evolutionary history for hormogastrid earthworms, showing the possibility of many dispersal and vicariance events and multiple faunal interchanges between land‐masses, which may reflect the biogeographical complexity of the Mediterranean Basin.