BEAST: Bayesian evolutionary analysis by sampling trees

Evaluation of global distribution, genetic evolution, and mammalian infectivity and pathogenicity of H13 and H16 avian influenza viruses

H13 and H16 subtype avian influenza viruses (AIVs) typically infect Charadriiformes, are widely distributed throughout coastal regions worldwide, and pose a risk of spill-over to mammals. Systematic research on the epidemiology, transmission dynamics, and biological characteristics of these subtypes remains limited. To address this gap, we analyzed 20 years of wild bird influenza surveillance data from China integrated with global influenza database information to reconstruct the global spatiotemporal distribution, transmission dynamics and public health implications of H13 and H16. During influenza surveillance, 28 H13 and 19 H16 viruses were isolated. The phylogenetic trees for the H13 and H16 viruses revealed that both subtypes could be classified into three distinct groups. Viruses from H13 Group A, H13 Group C, and H16 Group C demonstrated frequent genetic exchanges and intercontinental transmission on a global scale. Mapping host migration revealed overlap between virus spread and host migration pathways. Our results suggest that host migration is a key driver of widespread distribution, cross-regional spread, and gene exchange for some H13 and H16 lineages. Virus isolates exhibit high genetic diversity with rich genotypic variation. Most isolates carry mammalian-adaptive mutations, such as the G228S mutation in the HA protein. H13 and H16 isolates of multiple genotypes infected mice without prior adaptation and exhibited varying tissue tropism. In summary, these findings indicate that host migration patterns are closely associated with the evolution of H13 and H16 AIVs. The potential risk of mammalian infection is highlighted, as viruses carrying mammalian-adaptive mutations may lead to new infection cases.

Deciphering the patterns and timing of diversification of the genus Melanastera (Hemiptera: Psylloidea: Liviidae) in the Neotropics

Even after decades of research on diversification in the Neotropics, our understanding of the evolutionary processes that shaped Neotropical clades is still incomplete. In the present study, we used different divergence times and likelihood-based methods to investigate the influence of biogeography and host plant associations on the diversification of the most species-rich psyllid genus Melanastera (Liviidae) from the Neotropics as a model group of herbivorous insects. We used molecular phylogenetic data from seven gene fragments (four mitochondrial and three nuclear). The putatively monophyletic group of Neotropical Melanastera species has an estimated crown node age of 20.2 Ma (ML, CI 20.2-30.6) or 23.2 Ma (BI, 95 % HPD 16.6-32.6), with diversification occurring mainly in the Upper Miocene, although some species groups diversified in the Pliocene or Pleistocene. Biogeographic analysis suggests that the Neotropical Melanastera originated from the Pacific region of South and Central America. We detected a shift in diversification rates that likely occurred either at the time of origin of Melanastera or during the main colonisation of the Atlantic and Amazon Forests, followed by a subsequent slowdown in speciation rates. State-dependent speciation and extinction models revealed a significant relationship between this diversification shift and the shift of Melanastera to the plant families Melastomataceae and Annonaceae, reflecting the impact of host switching on speciation rates in this group. This period also coincides with several independent dispersal events from the Atlantic and Amazon Forests to other parts of the Neotropics. Taken together, the results of the current study suggest that diversification of Melanastera was facilitated by shifts to new host families, which may have promoted the dispersal of Melanastera into new adaptive zones with subsequent processes of local speciation.

New species of Ellipsomyxa (Bivalvulida: Ceratomyxidae) parasitizing the gallbladder of Ageneiosus ucayalensis (Siluriformes: Auchenipteridae) in the Brazilian Amazon region

The present study describes a new myxozoan species, Ellipsomyxa matosi n. sp. infecting the gallbladder of the catfish Ageneiosus ucayalensis, on Jutuba Island, municipality of Belém, state of Pará, Brazil. The new species was diagnosed based on morphological and molecular analyses. 33 specimens were examined between February and May 2023, and all (100 %) presented disporic plasmodia in the bile fluid, with ellipsoidal, slightly elongated mature myxospores, with a subtle valve projection in the apical region and a curved suture line, typical morphological characteristics of the genus Ellipsomixa. The polar capsules were pyriform and of equal size, with a subterminal opening and 6-7 polar tubule coils. No histopathological changes, lesions, or inflammatory responses were observed in the epithelial layer or any part of the tissue. PCA identified the proximity in spore length (SL) of the new species to E. amazonensis and E. papantla. The partial SSU rDNA sequence obtained was distinct from all other available sequences from species of this genus. The phylogenetic analysis obtained high nodal support, grouping the new species as an ancestor of the well-defined clade of Ellipsomyxa species described in the Amazon region.

How virus migration and meteorological elements shape the seasonality of influenza a/H3N2: A case study in China

Recent global influenza resurgences, escalating to pandemics, emphasize the urgency for effective vaccinations. Despite their efficacy, vaccines offer limited protection against A/H3N2 variants. Thus, elucidating the spatial patterns and underlying drivers of A/H3N2 seasonality is critical for its management. However, the mechanisms governing this seasonality are not fully understood. The study conducted a collaborative and interdisciplinary analysis of influenza A/H3N2 epidemiology in China from 2012 to 2018, utilizing national influenza surveillance data, viral gene sequence data, and meteorological information. We initially examined the spatiotemporal distribution of influenza A/H3N2 across different temperate zones in China. Subsequently, we employed Bayesian "SkyGrid" reconstruction analysis to gain insights into the population dynamics of the influenza A/H3N2 virus within China's temperature zones. Additionally, we utilized generalized additive models (GAM) to assess the influence of meteorological factors on the seasonal prevalence of influenza A/H3N2. Our analysis of China's national influenza data revealed distinct seasonal patterns for A/H3N2: winter epidemics prevailed in temperate zones, while summer and autumn outbreaks occurred in subtropical and tropical areas. The seasonality of influenza A/H3N2 across China's diverse climatic zones is shaped by the interplay of virus migration and meteorological factors. Virus migration introduced new variant populations during seasonal epidemics of influenza A/H3N2 to different temperature zones in China, thereby seeding subsequent seasonal outbreaks. Our findings also indicate that meteorological elements trigger influenza A/H3N2 activity following virus migration. Moreover, the spatial variations in influenza A/H3N2 seasonality in China can be attributed to specific temperature thresholds, approximately 1 °C and 24 °C. These thresholds could serve as potential indicators for A/H3N2 prevalence. This insight is invaluable for tailoring region-specific prevention and control strategies in China and other regions with similar environmental conditions.

Disentangling serial chloroplast captures in willows

PREMISE

Chloroplast capture is a process through which the chloroplast of a focal species is replaced by the chloroplast from another species during repeated backcrossing of an initial hybrid. Here we investigated serial chloroplast capture from Salix nigra in willows during sequential hybridization events that led to the capture of the same chloroplast lineage across multiple Salix species.

METHODS

Previously generated sequences of nuclear and chloroplast regions from several Salix species were used to identify cases of cytonuclear phylogenetic discordance, a pattern indicating chloroplast capture. Serial chloroplast captures were identified by comparing phylogenetic topologies of the chloroplast trees to discriminate among (1) a single chloroplast capture and subsequent speciation of the lineage with the captured chloroplast, (2) multiple chloroplast captures from the same parent species, and (3) serial chloroplast captures. We also looked for hybridization in genes involved in cytonuclear interactions and in photosynthesis.

RESULTS

We identified cases of serial chloroplast capture and speciation after chloroplast capture in Salix. Although these chloroplast capture events were accompanied by signals of hybridization in the nuclear genomes, nuclear genes that functionally interact with chloroplast genes and nuclear genes involved in photosynthesis were no more likely to introgress in species with chloroplast captures than in species without chloroplast captures.

CONCLUSIONS

This study illuminates the complex evolution of the chloroplast genomes in Salix and the potential for hybridization and introgression to influence genomic evolution.

Evolutionary dynamics and codon bias analysis of canine circovirus: Insights into global spread and host adaptability

Circoviruses are relatively new pathogens, and new circoviruses are constantly being discovered, with a growing range of hosts. Recently, canine circovirus (CanineCV) was reported to infect cats and badgers, further broadening its host range. Previous studies on the evolution and dissemination of CanineCV were fragmented. Here, when conducting a metagenomic analysis of shelter dogs, we identified a canine circovirus positivity rate of 32.4% and obtained three new viral strains. Furthermore, we integrated publicly available viral sequences and employed multiple bioinformatic software tools to analyze the evolution, codon usage bias, recombination, origin, spatiotemporal distribution and host adaptability of CanineCV. In this study, CanineCV could be divided into five distinct phylogenetic clades, named as China-I, China-II, Cosmopolitan, EA, and SEA clades. The extensive inter-clade recombination was observed, which plays an important role in viral evolution, while based on existing sequence information, CanineCV most likely originated in Norway from Vulpes vulpes in 1950.7. Notably, CanineCV exhibits greater adaptability to human hosts compared to previously documented hosts, as indicated by host adaptability indices, suggesting that this virus may possess zoonotic potential. In summary, our study elucidates the phylogeography and evolutionary dynamics of CanineCV and underscores the importance of investigating its potential for zoonotic transmission.

Evolutionary trajectories of Nipah virus: Evaluating the antiviral efficacy of Kabasura Kudineer Chooranam

Nipah virus (NiV) is a highly contagious zoonotic pathogen causing severe encephalitis and respiratory illnesses in humans. With a high fatality rate and no FDA-approved treatments, NiV poses a significant public health threat. This study conducts a comprehensive Bayesian phylogenetic analysis of all publicly available NiV genomes since the first human case. Additionally, a protein-protein interaction (PPI) network analysis focusing on Pteropus species was performed to identify potential therapeutic targets. High-throughput virtual screening assessed the inhibitory potential of Kabasura Kudineer Chooranam phytocompounds against these targets. Molecular dynamic simulations (MDS) were conducted to evaluate the stability and dynamic characteristics of NiV proteins bound to specific inhibitors. Bayesian phylogenetic analysis of 280 NiV genomes revealed two distinct clades among Indian isolates, highlighting significant regional diversity. Notably, the latest strain, OM135495, along with other NiV variants in Kerala, underscores the virus's rapid genetic evolution since 2015. The PPI network identified NiV-F, NiV-G, and NiV-N as key therapeutic targets. Among the tested phyto compounds, Vasicinone and Piperine exhibited strong binding affinities (-4.51 to -5.96 kcal/mol) and enhanced stability during MDS, suggesting their potential as antiviral agents. These findings indicate that phyto compounds may serve as viable alternatives for NiV treatment, paving the way for novel drug development. However, further validation through laboratory and animal studies is essential. This study enhances our understanding of NiV evolution, informs public health strategies, and contributes to preparedness for future outbreaks.

Strong bat predation and weak environmental constraints predict longer moth tails

Elaborate traits evolve via intense selective pressure, overpowering ecological constraints. Hindwing tails that thwart bat attack have repeatedly originated in moon moths (Saturniidae), with longer tails having greater anti-predator effect. Here, we take a macroevolutionary approach to evaluate the evolutionary balance between predation pressure and possible limiting environmental factors on tail elongation. To trace the evolution of tail length across time and space, we inferred a time-calibrated phylogeny of the entirely tailed moth group (Actias + Argema) and performed ancestral state reconstruction and biogeographical analyses. We generated metrics of predation via estimates of bat abundance from nearly 200 custom-built species distribution models and environmental metrics via estimates of bioclimatic variables associated with individual moth observations. To access community science data, we developed a novel method for measuring wing lengths from un-scaled photos. Integrating these data into phylogenetically informed mixed models, we find a positive association between bat predation pressure and moth tail length and body size, and a negative association between environmental factors and these morphological traits. Regions with more insectivorous bats and more consistent temperatures tend to host longer-tailed moths. Our study provides insight into tradeoffs between biotic selective pressures and abiotic constraints that shape elaborate traits across the tree of life.

Why the Long "Horns"? Fine-Scale Morphology Suggests Tactile Demands Contributed to the Exaggeration of Male Longhorned Beetle Antennae (Coleoptera: Cerambycidae)

Insect antennae are covered in hairlike sensilla that detect diverse environmental cues. Selection on these functions has produced a bewildering variety of antennal forms, including many examples of sexual dimorphism (SD). Antenna length SD is particularly common, but poorly understood, in longhorned beetles (Coleoptera: Cerambycidae). Extremely elongate male antennae may extend the reach of individuals searching for mates, enabling rapid recognition via antennal contact. Alternatively, they may increase sensitivity to airborne pheromones by bearing more olfactory sensilla. We tested these hypotheses by modeling sensillum distributions and abundances across species and sexes of Anoplistes, a cerambycid genus with extensive variation in antenna length and SD. We found limited evidence that olfactory sensillum abundance scales with antenna segment length; instead, mechano- and contact chemosensory sensilla cluster near the antenna tip, consistent with contact-mediated mate recognition. If the tip segment serves an important tactile role, that may explain why it is exceptionally elongated in males of several species with long, sexually dimorphic antennae. In other Anoplistes species with strong antennal SD, however, all segments exhibit similar levels of dimorphism. Collectively, our results suggest that alternative pathways to antenna SD evolved rapidly in Anoplistes, perhaps due to different patterns of selection on tactile sensation.

Estimating the impact of direct acting antiviral therapy on the prevalence of hepatitis C virus infection using phylogenetics

INTRODUCTION

Australia has provided unrestricted subsidized access to direct-acting antiviral (DAA) treatment for hepatitis C virus (HCV) infection since 2016. Epidemiological surveillance estimates suggest prevalence of chronic HCV infection has declined since 2016, but these estimates are not separated by genotype and may not capture 'hidden' infected populations, notably the most marginalized groups affected, including people who inject drugs and people in prison. This study used phylogenetics to assess whether epidemiological estimates of declining HCV prevalence in the prisons of New South Wales, Australia due to DAA scale up could be reproduced.

METHOD

Near-full-length 280 HCV consensus sequences (GT1a: n = 140, GT3a: n = 140) sampled between 2006 - 2019 from two prison-based cohort studies in NSW were used for phylogenetic estimates. These included 110 acute infection sequences (GT1a: n = 48, GT3a: n = 62) which were considered in a separate sensitivity analysis given the differences in virus mutation rates in acute and chronic infection. Changes in the effective population size of infected people for each genotype were explored with BEAST software suite (v1.10) using a coalescent Bayesian skyline approach.

RESULTS

Both the main and sensitivity analyses for GT3a showed a reduction in the effective population size with the latter showing a 36 % decline between 2011-2019 which is more concordant with the decline estimated from non-phylogenetic methods. A decline of similar magnitude was not demonstrated for GT1a. Overall, the analyses using acute infection sequences only were closer to the trends of independent epidemiological estimates.

CONCLUSIONS

An adequately powered Bayesian evolutionary analysis using acute stage infection sequences may reproduce the decline in HCV infections observed by traditional epidemiological methods during DAA scale up.

Epidemiology and evolutionary dynamics of H9N2 avian influenza virus in Bangladesh

Low pathogenicity avian influenza (LPAI) H9N2 has been enzootic in Bangladeshi poultry since 2006. H9N2 outbreaks can decrease egg production and growth and pose a risk to human health. The role of avian hosts in the persistence, evolution, and dispersion of H9N2 is poorly understood in Bangladesh. Hence, this study unveils the intricate role of major host species in virus maintenance and evolution and the temporal and seasonal patterns of H9N2 in Bangladesh from 2006 to 2023. Multinomial logistic regression analysis indicated that the circulation of H9N2 in different species and interfaces is significantly influenced by the seasons. Bayesian phylogenetic analysis of H9N2 sequences in Bangladesh revealed two distinct lineages: G1 and Eurasian. The G1 lineage split into two clusters, coexisting until 2019, at which point only one cluster persisted. Bayesian phylodynamic analysis of G1 lineage unveiled frequent bidirectional viral transitions among ducks, chickens, and quails. Chickens might be a pivotal source of H9N2 in Bangladesh, with a higher number of viral transitions from chickens to ducks and quails. Quails appear to acquire most of their viral transitions from chickens rather than ducks, suggesting that quail epizootics are primarily triggered by spillover events from chickens. Our results suggest viral circulation in commercial chickens despite vaccination. The vaccination approach should be revised, assess vaccine efficacy, and extension of vaccination to backyard chickens and quails.

Human de novo mutation rates from a four-generation pedigree reference

Understanding the human de novo mutation (DNM) rate requires complete sequence information1. Here using five complementary short-read and long-read sequencing technologies, we phased and assembled more than 95% of each diploid human genome in a four-generation, twenty-eight-member family (CEPH 1463). We estimate 98-206 DNMs per transmission, including 74.5 de novo single-nucleotide variants, 7.4 non-tandem repeat indels, 65.3 de novo indels or structural variants originating from tandem repeats, and 4.4 centromeric DNMs. Among male individuals, we find 12.4 de novo Y chromosome events per generation. Short tandem repeats and variable-number tandem repeats are the most mutable, with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 16% of de novo single-nucleotide variants are postzygotic in origin with no paternal bias, including early germline mosaic mutations. We place all this variation in the context of a high-resolution recombination map (~3.4 kb breakpoint resolution) and find no correlation between meiotic crossover and de novo structural variants. These near-telomere-to-telomere familial genomes provide a truth set to understand the most fundamental processes underlying human genetic variation.

The evolutionary history and timeline of mites in ancient soils

Acariform mites play a crucial role as primary soil decomposers, impacting the carbon cycle. However, the timing of their diversification is uncertain, with estimated dates ranging from the Precambrian (no land plants) to the Carboniferous (diverse terrestrial ecosystems). One factor affecting these time estimates is an uncertain phylogenetic position of the earliest unequivocal fossil mites from the Devonian Rhynie Chert, which have been classified in five modern families and three suborders. Here, we thoroughly examine these specimens, assign them to a single species Protacarus crani (family Protoacaridae, fam. nov., suborder Endeostigmata) and integrate this information into a time-calibrated phylogenetic analysis. Our phylogeny suggests a Cambrian basal divergence of Acariformes (508-486 Ma), coinciding with the land colonization by bryophytes. At this time, the mites' ecological niches were probably diversified beyond the upper soil. Our study provides temporal context, improves the accuracy of fossil dating, and underscores the importance of mites' diverse habitats and their potential roles in soil food webs.

Genome evolution of Kaposi sarcoma-associated herpesvirus (KSHV)

Kaposi sarcoma (KS) is the most common cancer in people living with HIV (PLWH), particularly in sub-Saharan Africa (SSA), where Kaposi sarcoma herpesvirus (KSHV or human herpesvirus 8 [HHV-8]) is endemic. In KSHV endemic areas, the overall survival of KS patients has changed little over the past 20 years. A phylogenetic analysis of available full-length viral genomes (n = 164) identified two different virus lineages that co-circulate in KSHV endemic regions today. Their sequences differ from the GenBank reference sequence and those of common laboratory strains, which originated in the 1990s in the US and Europe. Targeted short-read sequencing accuracy was validated by PacBio-based long-read sequencing to resolve repeats. This analysis identified over 1,000 single nucleotide variants (SNV) in a new 14-member sequence collection from tumor biopsies and blood in Malawi with 127 ± 32 (median ± SD) SNV per genome. Most were private, i.e., specific to one individual's virus. Within each of the two lineages, KSHV continues to evolve over time and across national borders by genetic drift and recombination. Analyses of shared SNVs by AlphaFold2 predicted some changes in the conformation of key viral proteins. These findings may help our understanding of herpesvirus evolution.

IMPORTANCE

To understand viruses, the field needs to know their genetic makeup. To develop mechanistic models, targeted therapies, and vaccines, we need comprehensive and up-to-date sequence information on the viral strains that circulate where the diseases appear today. Our knowledge of Kaposi sarcoma herpesvirus (KSHV) sequence distribution and evolution is behind that of other human herpesviruses and RNA viruses. Here, we add to community knowledge using new technologies and artificial intelligence.

Molecular epidemiological surveillance of respiratory syncytial virus infection in Myanmar from 2019 to 2023

To evaluate genetic changes in respiratory syncytial virus (RSV) between 2019 and 2023, we analyzed RSV strains from Myanmar before and after the COVID- 19 pandemic. Real-time polymerase chain reaction (RT-PCR) positive samples from children presenting with acute respiratory infections at outpatient clinics in Yangon were sequenced to determine the genotype. Phylogenetic and molecular evolutionary analyses were conducted using the Bayesian Markov Chain Monte Carlo method to construct the time-scale Maximum Clade Credibility tree. Of 1127 samples, 104 (9.2%) RSV-A and 233 (20.7%) RSV-B were positive by RT-PCR. There was an absence of a notable epidemic in 2020, a temporal shift with a surge of RSV-A in the 2021 outbreak, a lack of expected cases in 2022 and a substantial resurgence of RSV-B in 2023. The genotype of RSV-A was mainly A.D.3 lineage through the study period, while RSV-B were B.D.4.1.1 and B.D.E.1. RSV-A showed that the same lineage persisted within Myanmar throughout the pandemic, leading to a large outbreak post-COVID. In contrast, RSV-B strains appear to have temporarily disappeared during the pandemic, but subsequently, globally circulating strains likely entered Myanmar, resulting in a major outbreak in 2023. The estimated evolutionary rate at the G-ectodomain for RSV-A was 7.76 × 10⁻³ and RSV-B was 5.67 × 10⁻³ substitutions/site/year. Strengthening genomic surveillance will likely support comparisons of circulating strains with those in other countries and facilitate the introduction of vaccines and other interventions.

Genome-wide insights into the evolutionary history of conserved photosynthetic NDH-1 in cyanobacteria

The integration of novel components into functional multi-subunit protein complexes is a key evolutionary strategy for enhancing stability, activity, and adaptation to oxidative stress. This is exemplified by the evolution of the conserved photosynthetic NDH-1 (cpNDH-1) complex, though its precise evolutionary history remains unresolved. In this study, we constructed a time-calibrated phylogenetic tree of cyanobacteria to trace the evolutionary trajectory of cpNDH-1. By mapping the orthologous of oxygenic photosynthesis-specific (OPS) subunits onto this tree, we found that the cpNDH-1 complex progressively acquired OPS subunits. Specifically, during the transition from non-photosynthetic to thylakoid-less photosynthetic cyanobacteria, cpNDH-1 incorporated OPS subunits NdhM, NdhN, NdhO, NdhP, and NdhS. Subsequently, NdhL, NdhQ, and NdhV were added as thylakoid-bearing photosynthetic cyanobacteria evolved. Our analysis reveals that the emergence of oxygenic photosynthesis was closely linked with the progressive incorporation of OPS subunits into cpNDH-1. We propose a two-step model for the evolution of these subunits, identifying potential driving factors behind this process. Genome-wide sequence analysis and structural predications further suggest that the OPS cpNDH-1 genes either evolved de novo or arose from modifications of existing genes. Collectively, these findings provide a robust framework for understanding the evolutionary emergence of OPS subunits in cyanobacterial cpNDH-1, underscoring the acquisition of new subunits as a critical adaptation to oxidative environments during the evolution of oxygenic photosynthesis.

Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification

The microbiome of the gut is a complex ecosystem that contains a wide variety of microbial species and functional capabilities. The microbiome has a significant impact on health and disease by affecting endocrinology, physiology, and neurology. It can change the progression of certain diseases and enhance treatment responses and tolerance. The gut microbiota plays a pivotal role in human health, influencing a wide range of physiological processes. Recent advances in computational tools and artificial intelligence (AI) have revolutionized the study of gut microbiota, enabling the identification of biomarkers that are critical for diagnosing and treating various diseases. This review hunts through the cutting-edge computational methodologies that integrate multi-omics data-such as metagenomics, metaproteomics, and metabolomics-providing a comprehensive understanding of the gut microbiome's composition and function. Additionally, machine learning (ML) approaches, including deep learning and network-based methods, are explored for their ability to uncover complex patterns within microbiome data, offering unprecedented insights into microbial interactions and their link to host health. By highlighting the synergy between traditional bioinformatics tools and advanced AI techniques, this review underscores the potential of these approaches in enhancing biomarker discovery and developing personalized therapeutic strategies. The convergence of computational advancements and microbiome research marks a significant step forward in precision medicine, paving the way for novel diagnostics and treatments tailored to individual microbiome profiles. Investigators have the ability to discover connections between the composition of microorganisms, the expression of genes, and the profiles of metabolites. Individual reactions to medicines that target gut microbes can be predicted by models driven by artificial intelligence. It is possible to obtain personalized and precision medicine by first gaining an understanding of the impact that the gut microbiota has on the development of disease. The application of machine learning allows for the customization of treatments to the specific microbial environment of an individual.

Phylogenetic characterization of the pork tapeworm Taenia solium in Japan: implications for the enigmatic evolutionary history

Taenia solium is a tapeworm of the family Taeniidae that causes neurocysticercosis, a serious zoonotic disease in humans. Its life cycle involves pigs and wild boars as intermediate hosts and humans as the sole definitive host. Since poor sanitation and free-roaming pigs contribute to maintaining its life cycle, cysticercosis is endemic in developing countries across Asia, Africa, and Latin America, while local transmission is generally absent in developed countries. However, we unexpectedly identified three cases of cysticercosis in wild boars in Japan between 2014 and 2023. Genetic analyses were performed on six cysticerci collected from two wild boars independently captured in 2023. Phylogenetic analysis using three nuclear DNA markers confirmed that the cysticerci were indeed T. solium. Mitogenome sequencing from these cysticerci yielded six complete mitogenomes, each 13,712 bp in length and identical to each other. Haplotype network analysis using mitochondrial cox1 and cob sequences revealed that the cysticerci in Japan possess a haplotype distinct from haplogroups in other endemic regions, i.e., haplogroups in Asia, Africa/America, and Bhutan, indicating that the T. solium population is divided into at least four haplogroups. Subsequent phylogenetic inference from the mitochondrial 12 protein-coding genes demonstrated that the Japanese haplotype diverged from both the Asian and African/American haplogroups before the divergence of these two major haplogroups in the Early to Middle Pleistocene. Our findings indicate that the T. solium life cycle can be maintained in regions generally considered non-endemic, highlighting an overlooked risk of local transmission in developed countries. Furthermore, the genetic diversity and phylogenetic relationships revealed in this study may provide evidence for revisiting the "Out of Africa" hypothesis for T. solium. Comprehensive mitogenomic analyses based on additional specimens would hold the key to unraveling the evolutionary history of this tapeworm, which currently uses humans as its sole definitive host.

Global population dynamics and evolutionary selection in classical swine fever virus complete genomes: insights from Bayesian coalescent analysis

Classical swine fever virus (CSFV) is a pathogen that affects pigs and wild boars. This contagious RNA virus is a high threat to swine industries throughout the world because it has high mortality and morbidity rates, leading to economic losses. Although some studies have analyzed whole-genome sequences, but often focus on isolates from only a few countries, while others started with whole-genome analysis before narrowing down to specific gene region like E2. In addition, several studies have predominantly focused on isolated geographic regions. Our study leverages a global dataset of 220 CSFV whole-genome sequences retrieved from the NCBI repository along with two CSFV complete genome sequence from our laboratory (Accession Number: MH734359.1 and OR4282229.1) and carefully curated to 66 sequences. The refined dataset was subjected to Bayesian analysis along with selection pressure analysis. The outcome of this experiment, the mean substitution rate was estimated at 2.06 × 10-3 substitutions/site/year with the Highest Posterior Density (HPD) (95% HPD 6.8012 × 10-4 to 3.3044 × 10-3), and the estimated average time to the most recent common ancestor (tMRCA) for the analyzed dataset was the year 1877 (95% HPD 1833.8181-1932.3176). Among the curated dataset, 2 CSFV complete genome sequences (Accession Number: MH734359.1 and OR428229.1) from our laboratory showed a Chinese origin. In addition, pervasive and episodic selection pressure revealed that both had ongoing diversifying natural positive selection, which could lead to increased genetic diversity and possibly emergence of the new lineage. This potential information could be used for future evaluation of strategies to control emerging new genotypes of CSFV with high mortality and morbidity.

Emergence, persistence, and positive selection of yellow fever virus in Colombia

Yellow fever virus (YFV) is an arbovirus that causes acute febrile illness (AFI), in tropical areas of South America and Africa. Through a 2020-2023 AFI study in Leticia, Colombia, leveraging metagenomic next-generation sequencing (mNGS), we identified and isolated YFV (LET1450). Phylogenetic analysis showed this strain belongs to South American genotype II (SamII), linked to Peruvian and Bolivian sequences emerging around 1989. Phylodynamic analysis indicates these strains, with a unique genetic makeup, could have reduced vaccine susceptibility, and due to positive Darwinian selection have an enhanced adaptive capacity. Antigenic analysis identified additional immune-evasive traits and this strain's potential for wider Latin American spread. Phylogeographic reconstruction demonstrated the persistence of YFV in Colombia is not due to repeated external introductions, but results from continuous, cryptic internal circulation. This study highlights the crucial role of mNGS in monitoring emerging strains and underscores the need for genomic surveillance of YFV and other arboviral infections.

Dated Phylogeny of Banisteriopsis (Malpighiaceae) Suggests an Ancient Colonization of the Cerrado and No Evidence of Human Manipulation in the Origin of B. caapi

Banisteriopsis is a genus in the Malpighiaceae family with 61 species, notable for including ritualistic taxa such as B. caapi (Spruce ex Griseb.) C.V. Morton, one of the main components of Ayahuasca tea. We analyzed 38 Banisteriopsis species, representing more than 60% of the genus, to investigate its geographical origin, diversification period, and colonization routes in the Neotropics. Plastid genes (matK, ndhF, and rbcL) and nuclear regions (ETS, ITS, and PHYC) were used in our analyses. Divergence time analyses were performed using Bayesian inference with a relaxed molecular clock and ancestral area reconstruction. Our results show that Banisteriopsis originated in the Miocene approximately 22 million years ago, and its diversification coincides with the expansion of dry areas in South America. Banisteriopsis began colonizing the Cerrado earlier than most other plants, and the history of the genus reveals that the biome served as a source of species for Neotropical rainforests. Our results also indicate a probable ancient origin for B. caapi, with no evidence of human manipulation in its diversification, and they reinforce archaeological evidence of a millennia-old exchange of uses among Amazonian peoples.

Molecular phylogeny and biogeography of the genus Tulipa (Amana spp.) in East Asia

The East Asian tulips (Amana spp.), which are endemic to East Asia, include the species A. edulis, recognized as the source of the traditional Chinese medicine (TCM) known as "Guangcigu." In this study, we collected 50 samples representing six Amana species: A. edulis, A. erythronioides, A. anhuiensis, A. kuocangshanica, A. wanzhensis, and A. baohuaensis, across China and sequenced their complete chloroplast genomes. Phylogenetic analyses based on 74 shared protein-coding sequences in the chloroplast genome, along with divergence time estimations and biogeographic studies, have yielded several key findings. First, Amana spp. is confirmed to be monophyletic, having originated in the Late Miocene approximately 95% confidence interval of 5.63-12.52 million years ago, with diversification occurring within the 95% confidence interval of 2.36-4.68 million years ago in the mid-Pliocene, primarily in the Anhui and Zhejiang provinces. Second, Amana spp. comprise six valid species, each exhibiting varying degrees of dispersal into adjacent regions. Third, A. edulis, which emerged in the mid-Pliocene, has significantly expanded its range, colonizing the western parts of Jiangsu, Henan, and Jiangxi provinces and extending into northeastern China, North Korea, and Japan. This broad distribution, in comparison to other Amana species, is likely attributable to the evolutionary effects of the East Asian monsoon climate, which was intensified by the uplift of the Qinghai-Tibet Plateau. Analysis of chloroplast DNA markers revealed notable differences between A. edulis and other species, providing a reliable method for identifying Guangcigu and ensuring the safe use of this TCM.

The Ongoing Epidemics of Seasonal Influenza A(H3N2) in Hangzhou, China, and Its Viral Genetic Diversity

This study examined the genetic and evolutionary features of influenza A/H3N2 viruses in Hangzhou (2010-2022) by analyzing 28,651 influenza-like illness samples from two sentinel hospitals. Influenza A/H3N2 coexisted with other subtypes, dominating seasonal peaks (notably summer). Whole-genome sequencing of 367 strains was performed on GridION platforms. Phylogenetic analysis showed they fell into 16 genetic groups, with multiple clades circulating simultaneously. Shannon entropy indicated HA, NA, and NS gene segments exhibited significantly higher variability than other genomic segments, with HA glycoprotein mutations concentrated in antigenic epitopes A-E. Antiviral resistance showed no inhibitor resistance mutations in PA, PB1, or PB2, but NA mutations were detected in some strains, and most strains harbored M2 mutations. A Bayesian molecular clock showed the HA segment exhibited the highest nucleotide substitution rate (3.96 × 10-3 substitutions/site/year), followed by NA (3.77 × 10-3) and NS (3.65 × 10-3). Selective pressure showed A/H3N2 strains were predominantly under purifying selection, with only sporadic positive selection at specific sites. The Pepitope model demonstrated that antigenic epitope mismatches between circulating H3N2 variants and vaccine strains led to a significant decline in influenza vaccine effectiveness (VE), particularly in 2022. Overall, the study underscores the complex circulation patterns of influenza in Hangzhou and the global importance of timely vaccine strain updates.

Detection and molecular characterization of dengue among patients suspected of having malaria in Timika, Central Papua, Indonesia

BACKGROUND

Dengue and malaria are major public health problems in Indonesia. Dengue is hyperendemic nationwide, while malaria remains endemic in specific regions, especially in eastern Indonesia. Timika in Central Papua province is a highly malaria-endemic area; however, this city is historically known as a low endemic area for dengue. With the increasing incidence of dengue in Papua, this study aimed to assess dengue prevalence, possible co-infection and to molecularly characterize the dengue virus (DENV) in patients suspected of having malaria.

METHODS

Archived samples of patients suspected of having malaria were screened for dengue using RT-PCR. Dengue serological and antigen detection was performed and whole genome sequencing was employed to determine the genetic characteristics of viruses. Detection of other arboviruses was also performed.

RESULTS

Among 119 patients, 30 (25.2%) were positive for dengue. Most samples (n=29) were infected by DENV-3, while one was positive for DENV-2. Dengue and malaria co-infections were found in six patients. Phylogenetic analysis classified DENV-2 as the Cosmopolitan genotype that is closely related to strains from the Indonesian city of Makassar, while DENV-3 was classified as Genotype I, which is closely related to a strain from Singapore.

CONCLUSIONS

Dengue significantly contributes to febrile illness among patients suspected of having malaria in Timika, Central Papua. Virus importation from surrounding regions is likely to contribute to the dispersion of DENV into eastern parts of Indonesia. Our findings reveal the underestimation of this viral disease in a highly malaria-endemic area.

Dengue dynamics in Bali: Serotype shifts, genotype replacement and multiple virus lineage circulation in the last 10 years

BACKGROUND

Bali, one of the world's most popular tourist destinations, is hyper-endemic to dengue, an acute febrile illness caused by infection with dengue virus (DENV). Outbreaks of dengue occur annually with worrisome rates of morbidity and mortality. Despite this, comprehensive and continuous virus surveillance is yet to be established. We conducted DENV serotype and genotype surveillance in Bali to monitor viral transmission dynamics.

METHODS

We enrolled febrile patients with dengue clinical symptoms in hospitals in Denpasar, Bali. Clinical evaluations and laboratory assessments were conducted, and blood samples were collected. DENV serotypes were determined using RT-PCR, and genotyping was performed by sequencing the envelope protein gene and the complete genomes. Subsequently, phylogenetic analyses were conducted to analyse the recent data alongside retrospective sequence data.

RESULTS

A total of 62 and 66 dengue patients were recruited during 2018-2020 and 2022, and from these, we obtained DENV serotype data for 49 and 48 individuals, respectively. Among the DENV analysed, the most prevalent serotype in 2018-2020 was DENV-1 (30%) and shifted to DENV-3 (57.6%) in 2022. When compared to data from the last 10 years, serotype shifting was clearly observed. We sequenced the genomes of 60 isolates and observed the presence of multiple virus lineages and the replacement of Genotype IV of DENV-1 with Genotype I. The Cosmopolitan, Genotype I and Genotype II remained the predominant genotypes for DENV-2, DENV-3 and DENV-4, respectively.

CONCLUSION

We reveal that DENV serotype predominance in Bali has been shifting in the past 10 years. While genotype replacement occurred, continuous circulation of local endemic viruses was responsible for the annual outbreak of dengue. These findings indicate the genetic diversity and dynamic nature of DENV circulating in Bali. Routine virus surveillance is important to understand the cyclical patterns of DENV serotypes that is useful to predict the future outbreaks.

Genomic epidemiology and antimicrobial resistance reveal local transmission dynamics of enteric fever in Shenzhen, one of the mega cities in China

OBJECTIVES

Outbreak of enteric fever and the spread of antimicrobial-resistant Salmonella Typhi and S. Paratyphi pose significant public health challenges in low- and middle-income countries. Understanding the transmission dynamics of these pathogens is essential for developing effective control strategies.

METHODS

We conducted phylogenomic analyses and integrated epidemiological data from 135 S. Typhi and 271 S. Paratyphi A isolates collected in Shenzhen from 2001 to 2017. Phylogenetic and temporal analyses were performed to identify prevalent genotypes and assess transmission patterns.

RESULTS

Analyses of S. Typhi isolates in Shenzhen revealed high genetic diversity, with genotypes 3.2.1 (37.8%) and 2.1.7 (20%) being most prevalent. Genotype 3.2.1 formed an independent lineage due to mutations in the quinolone resistance-determining region (QRDR). The multidrug-resistant haplotype 58 (genotype 4.3.1) has been present since 2006. S. Paratyphi A isolates were predominantly genotype 2.3.3 (98.5%). Pathogen exchange occurred with at least four other provinces. A cutoff of ≤3 single nucleotide polymorphisms (SNPs) was effective for outbreak investigation, and 22 genomic clusters were found, suggesting undetected outbreaks or transmission events. While 80% of isolates were susceptible to first-line antibiotics, 16.9% of S. Paratyphi A isolates were multidrug-resistant.

CONCLUSIONS

This study provides insights into the transmission dynamics of enteric fever in Shenzhen, underscoring the need for ongoing genomic surveillance to manage and control outbreaks effectively.

Host-Pathogen-Vector Continuum in a Changing Landscape: Potential Transmission Pathways for Bartonella in a Small Mammal Community

Bacterial infections account for a large proportion of zoonoses. Our current understanding of zoonotic spillover, however, is largely based on studies from viral systems. Small mammals such as rodents and their ectoparasites present a unique system for studying several bacterial pathogens and mapping their spillover pathways. Using Bartonella spp. (a Gram-negative bacteria) as a model system within a rainforest human-use landscape, we investigated (1) ecological correlates of Bartonella prevalence in small mammal hosts and (2) evolutionary relationships between Bartonella spp. and various hosts and ectoparasites to gain insight into pathogen movement pathways within ecological communities. We detected Bartonella in five out of eight small mammal species and in 86 (40.56%) out of 212 individuals, but prevalence varied widely among species (0%-75.8%). Seven of the ten ectoparasite species found on these small mammals were positive for Bartonella. Interestingly, while Bartonella genotypes (15) in small mammals were host-specific, ectoparasites had nonspecific associations, suggesting the possibility for vector-mediated cross-species transmission. We also found that Bartonella prevalence in hosts was positively correlated with their aggregated ectoparasite loads, further emphasizing the crucial role that ectoparasites may play in these transmission pathways. Our cophylogenetic analysis and ancestral trait (host) reconstruction revealed incongruence between small mammal and Bartonella phylogenies, indicating historic host shifts and validating the potential for contemporary spillover events. We found that small mammal hosts in this fragmented landscape often move across habitat boundaries, creating a transmission pathway (via shared ectoparasites) to novel hosts, which may include synanthropic species like Rattus rattus. Our results highlight the necessity to disentangle the complex relationship among hosts, ectoparasites, and bacterial pathogens to understand the implications of undetected spillover events.

The effects of genome size and climate on basal metabolic rate variation in rodents

Basal metabolic rate (BMR) is the most commonly measured energetic variable in endothermic animals. Identifying the underlying factors driving interspecific variation in BMR remains a major question in the field of energetics. While body size (M) and taxonomic affiliation are the intrinsic factors that account for most of the interspecific variation in BMR, haploid genome size (C-value) is hypothesized to directly influence cell size and, indirectly, the specific metabolic rate. Climatic variables, mostly ambient temperature, have also been proposed as predictors of mass-independent BMR for endotherms. Therefore, in this study, we aimed to investigate the relative importance of intrinsic (C-value: CV) and extrinsic (climatic variables) factors as predictors of BMR in 67 rodent species in a phylogenetic context. The best ordinary least square (OLS) and phylogenetic generalized least squares (PGLS) models explaining interspecific variation in BMR included the variables logM, logCV, maximum temperature of the warmest month (Tmax), minimum temperature of the coldest month (Tmin) and net primary productivity (NPP). logM was the main determinant of logBMR variation in the rodents analyzed. Part of the remaining variation was attributed to a negative effect of genome size, explaining 14% of the BMR variance when Tmin was included in the model. As expected, one or two climatic variables were involved in explaining the remaining BMR variation (Tmin, Tmax and NPP). Our study highlights the importance of a denser sampling within vertebrate clades and the use of a phylogenetic context to elucidate the factors that contribute to explain BMR variation.

Phylogenetic minimum description length: an optimality criterion based on algorithmic complexity

Phylogenetic minimum description length (PMDL) is proposed as an optimality criterion for phylogenetic analysis. PMDL is based on algorithmic (Kolmogorov) information and the minimum description length principle. This criterion generates natural weighting functions (i.e. not being externally specified) for a diversity of phylogenetic graph, data and model types. PMDL is a generalized criterion that converges on existing forms of inference (i.e. parsimony, likelihood, Bayesian) in specific circumstances. Furthermore, as opposed to existing criteria, PMDL includes graph complexity allowing for the competition of hypotheses with myriad types of phylogenetic graphs (e.g. trees, networks, forests). Owing to its compound nature, PMDL allows for analytical model choice along with phylogenetic graph hypothesis while avoiding over-parameterization. Although uncomputable, heuristic methods are presented for the calculation of upper bounds on the algorithmic information content of a phylogenetic hypothesis. Examples are presented demonstrating the approach.

Neolithic to Bronze Age human maternal genetic history in Yunnan, China

Yunnan in southwest China is a geographically and ethnically complex region at the intersection of southern China and Southeast Asia, and a focal point for human migrations. To clarify its maternal genetic history, we generated 152 complete mitogenomes from 17 Yunnan archaeological sites. Our results reveal distinct genetic histories segregated by geographical regions. Maternal lineages of ancient populations from northwestern and northern Yunnan exhibit closer affinities with past and present-day populations from northern East Asia and Xizang, providing important genetic evidence for the migration and interaction of populations along the Tibetan-Yi corridor since the Neolithic. Between 5500 and 1800 years ago, central Yunnan populations maintained their internal genetic relationships, including a 7000-year-old basal lineage of the rare and widely dispersed haplogroup M61. At the Xingyi site, changes in mitochondrial DNA haplogroups occurred between the Late Neolithic and Bronze Age, with haplogroups shifting from those predominant in the Yellow River region to those predominant in coastal southern China. These results highlight the high diversity of Yunnan populations during the Neolithic to Bronze Age.

A Million Years of Mammoth Mitogenome Evolution

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Evolution of Large Eyes in Stromboidea (Gastropoda): Impact of Photic Environment and Life History Traits

Eyes within the marine gastropod superfamily Stromboidea range widely in size, from 0.2 to 2.3 mm-the largest eyes known in any gastropod. Despite this interesting variation, the underlying evolutionary pressures remain unknown. Here, we use the wealth of material available in museum collections to explore the evolution of stromboid eye size and structure. Our results suggest that depth is a key light-limiting factor in stromboid eye evolution; here, increasing water depth is correlated with increasing aperture width relative to lens diameter, and therefore an increasing investment in sensitivity in dim light environments. In the major clade containing all large-eyed stromboid families, species observed active during the day and the night had wider eye apertures relative to lens sizes than species observed active during the day only, thereby prioritizing sensitivity over resolution. Species with no consistent diel activity pattern also had smaller body sizes than exclusively day-active species, which may suggest that smaller animals are more vulnerable to shell-crushing predators, and avoid the higher predation pressure experienced by animals active during the day. Within the same major clade, ancestral state reconstruction suggests that absolute eye size increased above 1 mm twice. The unresolved position of Varicospira, however, weakens this hypothesis and further work with additional markers is needed to confirm this result.

Molecular HIV Surveillance: Beyond Cluster Detection and Response

There has been significant controversy surrounding the use of HIV sequence data to identify outbreaks of HIV transmission since the initiation of molecular HIV surveillance (MHS) in the US. The current approach to MHS is comprehensive cluster detection and response (CDR), in which clusters of related infections are identified and used as the basis for cluster-based or population-based interventions. With CDR, there are ethical and stigma concerns around the impingement of individual privacy, as well as legal concerns around the inference of transmission in regions where HIV criminalization laws and statutes exist. Here we propose an alternative approach to the analysis of HIV sequence and public health data that focuses on regions and populations rather than clusters, and still provides useful data for public health agencies.

Morphological characterization and phylogenetic placement of Ramiconidium sinense gen. et sp. nov. (Microascaceae, Microascales)

The fungal diversity in environments closely related to human life and health has been largely overlooked. This study describs Ramiconidium sinense gen. et sp. nov., isolated during a survey of soil fungi from Guizhou Wildlife Park in China. A multi-locus phylogenetic analyses demonstrated that Ramiconidium forms a distinct clade (from all previously recognized genera) in the family Microascaceae. R. sinense differs from other taxa of the family by the absence of a sexual state, the absence of anellidic conidiogenous cells, the absence of conidiomata and the production of conidiophores bearing acropetal chains of 0-1-septate conidia. Comprehensive descriptions and detailed illustrations, as well as its taxonomical position based on the analysis of the nucleotide sequences of phylogenetically informative molecular markers, of this are presented in this study.

Historical biogeography of the Mugil cephalus species complex and its rapid global colonization

Our understanding of speciation processes in marine environments remains very limited and the role of different reproductive barriers are still debated. While physical barriers were considered important drivers causing reproductive isolation, recent studies highlight the importance of climatic and hydrological changes creating unsuitable habitat conditions as factors promoting population isolation. Although speciation in marine fishes has been investigated from different perspectives, these studies often have a limited geographical extant. Therefore, data on speciation within widely distributed species are largely lacking. Species complexes offer valuable opportunities to study the initial stages of speciation. Herein we study speciation within the Mugil cephalus species complex (MCSC) which presents a unique opportunity due to its circumglobal distribution. We used a whole-genome shotgun analysis approach to identify SNPs among the 16 species within the MCSC. We inferred the phylogenetic relationships within the species complex followed by a time-calibration analysis. Subsequently, we estimated the ancestral ranges within the species complex to explore their biogeographical history. Herein, we present a fully resolved and well-supported phylogeny of the MCSC. Its origin is dated at around 3.79 Ma after which two main clades emerged: one comprising all West Atlantic and East Pacific species and the other all East Atlantic and Indo-Pacific species. Rapid dispersal following an initial founder colonization from the West to the East Atlantic led to the population of all major realms worldwide in less than 2 Myr. Physical and climatic barriers heavily impacted the ancestral distribution ranges within the MCSC and triggered the onset of speciation.

Phylo2Vec: A Vector Representation for Binary Trees

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with n leaves to a unique integer vector of length n-1. The advantages of Phylo2Vec are 4-fold: (i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, (iii) quick and unambiguous verification if 2 binary trees are identical topologically, and (iv) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for ML inference on 5 real-world datasets and show that a simple hill-climbing-based optimization scheme can efficiently traverse the vastness of tree space from a random to an optimal tree.

Morphological Variability amid Genetic Homogeneity and Vice Versa: A Complicated Case with Humidophila (Bacillariophyceae) from Tropical Forest Soils of Vietnam with the Description of Four New Species

A total of 18 Humidophila strains isolated from soil samples from Cát Tiên National Park have been studied. Based on morphometric analysis and molecular data for the V4 18S rDNA and rbcL regions, we proposed the presence of four new species: H. vietnamica, H. paravietnamica, H. cattiensis, and H. concava. This is the first study that provides molecular data for such a large number of Humidophila strains. Furthermore, we encountered some Humidophila strains with clear morphological differences (which we assigned to several morphotypes) that cannot be separated using the selected genetic markers and cannot be attributed to phenotypic variations in one species; these require further study of their genetic structure. We also observed the opposite case, where in the absence of morphological differences, clear genetic differentiation is shown, which demonstrates the presence of cryptic taxa in our sample. The maximum differences for these strains were observed in the V4 18S rDNA region. Our results show that the effectiveness of commonly used genetic markers V4 18S rDNA and rbcL for separating species can vary greatly. Our study highlights the need to research different genetic markers and their use for proper species separation, as well as the genetic diversity of diatoms, and the need for further studies of intra- and interspecific genetic distances.

Multiple Dataset-Based Insights into the Phylogeny and Phylogeography of the Genus Exbucklandia (Hamamelidaceae): Additional Evidence on the Evolutionary History of Tropical Plants

Southeast Asia's biodiversity refugia, shaped by Neogene-Quaternary climatic shifts and the Tibetan Plateau uplift, preserve relict lineages like Exbucklandia (Hamamelidaceae). Once widespread across ancient continents, this genus now survives in Asian montane forests, offering insights into angiosperm diversification. Chloroplast haplotypes formed three clades-Clade I (E. tricuspis), Clade II (E. populnea), and Clade III (E. tonkinensis)-with E. longipetala haplotypes nested within II/III. Nuclear microsatellites (SSRs) identified two ancestral gene pools: E. populnea and E. tricuspis showed predominant ancestry in Pool A, while E. tonkinensis and E. longipetala were primarily assigned to Pool B. All taxa exhibited localized genetic admixture, particularly in sympatric zones. Divergence dating traced the genus' origin to tropical Asia, with northward colonization of subtropical China ~7 Ma yielding E. populnea and E. tonkinensis. Quaternary Glacial Cycles triggered southward expansions, chloroplast capture, and localized hybridization. Morphological, nuclear, and plastid molecular evidence supports reclassifying E. longipetala as E. populnea × E. tonkinensis hybrids lacking genetic cohesion and E. tricuspis as a distinct species with a mixed nuclear composition. This study highlights how paleoclimate-driven gene flow shaped the phylogeography of relict taxa in Southeast Asia and the urgency of habitat restoration to conserve Exbucklandia.

Evolutionary analysis and population dynamics in the global transmission of Kaposi's sarcoma-associated herpesvirus

With the widespread prevalence of Kaposi's sarcoma-associated herpesvirus (KSHV) globally, particularly in sub-Saharan Africa and the Mediterranean region, the open reading frame (ORF) K1 gene, a key gene for distinguishing different subtypes of KSHV, has been extensively studied for its diversity and sequence variations. In this study, we collected K1 gene sequences representing subtypes of KSHV worldwide in order to assess the global distribution of KSHV subtypes and to investigate the recombination and selection history of KSHV. Recombination and gene flow analysis indicated a minimum average recombination rate of 0.41 per site for the K1 gene. Recombination analysis indicated that 11 major recombination events had occurred, predominantly in subtypes A and C, while subtype B showed minimal involvement in recombination processes, consistent with the gene flow analysis. Using tip-dating methods, we estimated that the most recent common ancestor of KSHV emerged in the 12th century, while the currently globally prevalent subtypes appeared within the past three centuries. Its recent origin and rapid evolution indicate that KSHV is now undergoing strong selection and is in the process of adaptation.

First report of a xenoma-forming parasitic ciliate in a gastropod: The case of the invasive snail Pomacea canaliculata

The apple snail Pomacea canaliculata is native to South America and has been introduced into many regions outside its natural range. Despite being one of the world's 100 worst invasive species, little is known about the pathologies caused by parasites other than digeneans. Here, we identify and characterize a xenoma-forming ciliate in P. canaliculata from three waterbodies in the province of Buenos Aires, Argentina, using histology, transmission electron microscopy (TEM), and molecular analyses. Under a stereomicroscope, the xenomas appeared individually as white nodules measuring up to 2 mm in diameter. Of the 133 snails examined by histology, 23 were infected with xenomas (17 %) that occupied the connective tissue of most organs, with 74 % of these were located in the kidney. Snails from the three water bodies were infected. The highest prevalence was observed in the Mar del Plata Port Reserve Pond (25 %), followed by Los Padres Lake (16.4 %) and Pigüé-Venado Channel (14.4 %). Of the infected snails, 70 % had a low infection intensity (fewer than 10 xenomas per slide). No significant inflammatory response was observed in host tissues. However, in specimens with xenoma accumulations, significant tissue changes were observed, including organ enlargement in the gill lamellae, mantle border, and lung, as well as tubule compression and connective tissue replacement in the digestive gland. The host cell becomes hypertrophied, and its nucleus disintegrates. Although no cilia were observed in histological sections, TEM analysis revealed that the organisms had cilia near the cytostome and around the body, a large food vacuole, a macronucleus, and a micronucleus. Phylogenetic analysis of the SSU rDNA sequence placed the ciliate in the class Phyllopharyngea, showing the closest relationship to an uncultured eukaryote identified by BLAST. This is the fifth record of xenoma-inducing ciliates in mollusks and the first report in a gastropod.

The song of the Doto (Nudibranchia: Dotidae): newly documented diversity from the coast of California

Two new species of Doto (Heterobranchia: Dotidae) are described from the coast of California, Doto urak Gosliner & Adayapalam sp. nov. and Doto kwakwak Gosliner & Adayapalam sp. nov. These two species can be distinguished from their sympatric congeners by their color pattern, elaboration of the cerata and associated structures, their reproductive morphology and molecular data. Both are members of the Pacific and southern Atlantic clade of species, detected previously by molecular phylogenetic methods. Previous findings about reproductive specializations in Doto, particularly in the Pacific and southern Atlantic clade, are tested and were supported by the addition of new members to this clade. More systematic and molecular phylogenetic work still needs to be undertaken with Doto to fully understand species richness, diversification, and biogeographical relationships.

Population Genetics, Demographic History, and Potential Distributions of the New Important Pests Monolepta signata (Coleoptera: Chrysomelidae) on Corn in China

Monolepta signata are polyphagous pest widely distributed in China, and the damage as well as economic losses it caused were increasing in recent years. Knowledge of species diversity, population structure and habitat suitability could enhance the efforts of pest control. Here, we sampled the populations of M. signata in almost all of China's major corn-producing regions. A total of 568 sequences were obtained from each gene. There were 48, 29, and 30 haplotypes of COI, ITS2 and EF-1α, respectively. The genetic distance between the HuangHuaiHai population and other populations was the largest. There were 61.90%, 71.43% and 61.90% of Nm values smaller than 1 in COI, ITS2 and EF-1α, respectively, which indicated that gene flow between most populations was weak. The degree of differentiation in most populations of M. signata was relatively high. The population of M. signata has also experienced rapid expansion. Population history dynamic analysis showed that the effective population size of M. signata remained relatively stable before 0.075 Ma. There was a slow contraction trend from 0.075 to 0.010 Ma. It has been rapidly and continuously expanding since 0.010 Ma. Among the investigated geographical populations, the "yellow-spot type" was only present in the populations of southern and southwestern regions, while the "two-spot type" and "four-spot type" were widely distributed in all other geographical populations. Predictions of the potential distribution areas of M. signata indicated that the northeast and north China regions will remain being the high suitability areas of M. signata in the future. Our results will not only facilitate studies on the phylogeography of M. signata but also benefit the effective monitoring and management of this agricultural pest.

Phylogenetic Analysis of Chikungunya Virus Eastern/Central/South African-Indian Ocean Epidemic Strains, 2004-2019

CHIKV infection is transmitted by Aedes mosquitoes spp., with Ae. aegypti considered as the primary vector and Ae. Albopictus playing an important role in sustaining outbreaks in Europe. The ECSA-Indian Ocean Lineage (IOL) strain emerged in Reunion, subsequently spreading to areas such as India, the Indian Ocean, and Southeast Asia, also causing outbreaks in naive countries, including more temperate regions, which originated from infected travelers. In Italy, two authocthounous outbreaks occurred in 2007 (Emilia Romagna region) and 2017 (Lazio and Calabria regions), caused by two different ECSA-IOL strains. The phylogenetics, evolution, and phylogeography of ECSA-IOL-CHIKV strains causing the 2007 and 2017 outbreaks in Italy were investigated. The mean evolutionary rate and time-scaled phylogeny were performed through BEAST. Specific adaptive vector mutations or key signature substitutions were also investigated. The estimated mean value of the CHIKV E1 evolutionary rate was 1.313 × 10-3 substitution/site/year (95% HPD: 8.709 × 10-4-1.827 × 10-3). The 2017 CHIKV Italian sequences of the outbreak in Lazio and of the secondary outbreak in Calabria were located inside a sub-clade dating back to 2015 (95% HPD: 2014-2015), showing an origin in India. Continued genomic surveillance combined with phylogeographic analysis could be useful in public health, as a starting point for future risk assessment models and early warning.

Characteristics of the First Domestic Duck-Origin H12N8 Avian Influenza Virus in China

The H12 subtypes of avian influenza viruses (AIVs) are globally prevalent in wild birds, occasionally spilling over into poultry. In this study, we isolated an H12N8 virus from ducks in a live poultry market. Full genomic analysis revealed that the virus bears a single basic amino acid in the cleavage site of the hemagglutinin gene. Phylogenetic analysis revealed that the eight gene segments of the H12N8 virus belong to the Eurasian lineage and the HA gene was clustered with wild bird-originated H12 viruses, with its NP gene showing the highest nucleotide similarity to 2013-like H7N9 viruses. The H12N8 virus replicated effectively in both mammalian and avian cells without prior adaptation. Moreover, the H12N8 virus could infect and replicate in the upper respiratory tract of BALB/c mice without prior adaptation. The H12N8 virus replicated and transmitted inefficiently in both ducks and chickens and hardly triggered high hemagglutination inhibition (HI) antibody titers in the inoculated and contact animals. These results suggest that the wild bird-origin H12N8 virus has reassorted with viruses circulating in domestic poultry, but it inefficiently replicates and transmits in avian hosts. Our findings demonstrate that H12N8 AIV has emerged in domestic poultry, emphasizing the importance of active surveillance of AIVs in both wild and domestic birds.

Tracing more than two decades of Japanese encephalitis virus circulation in mainland China

Japanese encephalitis is a viral disease caused by the Japanese encephalitis virus (JEV), primarily affecting rural areas of Asia and western Pacific region. China remains one of the main epicenters, experiencing a significant burden of human and animal cases despite vaccination efforts. The ecology of this arbovirus is complex, involving Culex mosquitoes as primary vectors, wading birds as natural reservoirs, and pigs as amplifying hosts. Given the virus's epidemiological importance in China, combined with the country's expanding pig farming industry and diverse climates, investigating the virus spread and its environmental drivers is needed to address its persistent burden. In this study, we conducted phylogeographic analyses by combining publicly available JEV envelope gene sequences from China and other regions. Our reconstructions revealed multiple introduction events leading to various circulating JEV clades in China, with one predominant clade. Additionally, our analyses showed a diffusion capacity of JEV exceeding previous estimates for co-circulating arboviruses. These differences could be attributed to pig trade or bird migration, calling for further investigations into the drivers of JEV spread.

IMPORTANCE

Japanese encephalitis virus (JEV) is the cause of Japanese encephalitis, a significant health concern in China. Despite being one of the most studied mosquito-borne viruses, no previous studies have combined genomic and geographic data to investigate the spatial epidemiology and dispersal capacity of the virus. In this study, we analyzed genomic, geographic, and environmental data to trace the dispersal history of JEV in China and explore the environmental factors influencing its distribution. Our findings show that JEV circulates predominantly in areas with higher temperatures, dense human and pig populations, and favorable conditions for Culex mosquitoes. Notably, our analyses showed a higher diffusion capacity of JEV compared to co-circulating viruses, possibly driven by factors like pig trade and bird migration. Our analysis calls for improved genomic surveillance and establishes a baseline for future studies on the effects of climate change, agricultural practices, and bird migration on JEV circulation.

Decussiphycussinensis sp. nov. (Bacillariophyceae, Mastogloiales) - a new species described from China, with comments on phylogenetic position of the genus

During the study of freshwater diatom communities in Hainan Province, China, we uncovered an unknown diatom species of the genus Decussiphycus, which is described as Decussiphycussinensis sp. nov. herein. The description is based on LM and SEM investigations; morphologically, the new species is compared to other taxa belonging to the genus. We complemented the description with the results of a molecular analysis based on SSU rDNA and rbcL sequencing. Molecular data is acquired for Decussiphycus for the first time. Hereby, we discuss the phylogenetic relationships between this genus and its closest allies - Aneumastus and Mastogloia, demonstrating the affinity of Decussiphycus within the order Mastogloiales.

Characterization of the Complete Mitochondrial Genome of Three Satyrid Butterfly Species (Satyrinae:Amathusiini) and Reconstructed Phylogeny of Satyrinae

Satyrinae, one of the most species-rich groups within the Nymphalidae family, has traditionally relied on morphological characteristics for classification. However, this approach encounters challenges due to issues such as cryptic species and paraphyletic groups. Recent molecular phylogenetic studies have revealed the complex evolutionary history of Satyrinae, leading to the reclassification of the originally polyphyletic Satyrini into multiple independent tribes and confirming the monophyletic status of groups such as Amathusiini. Nevertheless, the phylogenetic relationships and divergence times of certain tribes remain contentious. This study focuses on three species of the Amathusiini tribe (Faunis aerope, Stichophthalma howqua, and Aemona lena), constructing a phylogenetic tree by sequencing the complete mitochondrial genome and integrating 13 protein-coding genes, including COI and ND5. The results indicate that the mitogenome lengths for the three satyrid species are 15,512 bp for Faunis aerope, 13,914 bp for Stichophthalma howqua, and 15,288 bp for Aemona lena. The genetic composition and sequencing of the newly obtained mitogenomes exhibit high conservation and are distinctive to this group of butterflies. Each of the three mitogenomes contains a characteristic collection of 37 genes along with an AT-rich region. Notably, the tRNA genes across these mitogenomes display a conventional cloverleaf configuration; however, the tRNASer stem (AGN) lacks the dihydrouridine (DHU) arm. The three species exhibit varying lengths of AT-rich regions, resulting in differences in their mitochondrial genome sizes. Finally, the phylogenetic analysis supports the relationships among the four tribes of Satyrinae as: (Satyrini + (Amathusiini + Elymniini)) + Melanitini.

Phylogenomic species delimitation of studfishes (Fundulidae: Fundulus): evidence for cryptic species in agreement with the central highlands vicariance hypothesis

The Central Highlands ecoregion of the eastern United States represents a hotspot of freshwater biodiversity, with replicated patterns of vicariant speciation east and west of the Mississippi River. Previous phylogeographic investigation of the studfishes (Fundulus subgenus Fundulus) revealed evidence for vicariant speciation in the Central Highlands, but data were limited to a small number of gene sequences generated with Sanger sequencing. We used double digest restriction-site associated DNA sequencing (ddRADseq) to improve resolution of phylogeographic patterns and better characterize population genetic variation. Our sample design included individuals from the Fundulus catenatus species group (F. catenatus, F. bifax, and F. stellifer) and two outgroup taxa (F. julisia and F. rathbuni). Phylogenetic analyses support a monophyletic F. catenatus complex and a sister relationship with Mobile Basin studfishes (F. bifax and F. stellifer). Population genomics and species delimitation tests provide evidence for three species-level subdivisions of F. catenatus. We describe F. catenatus as limited to the Tennessee River and its drainages, F. caddo sp. nov., in the Ouachita Highlands, and F. cryptocatenatus sp. nov., occupying the remainder of the range. Modally, F. catenatus was characterized by fewer left pectoral rays (16 vs. 17). Fundulus caddo sp. nov. had modally fewer anal rays (15 vs. 16) and lateral scale rows (13 vs. 14). Fundulus cryptocatenatus sp. nov. was characterized by modally higher dorsal rays (15 vs. 14) and fewer caudal rays (16 vs. 17). The geographic distribution is likely the result of multiple pre-Pleistocene vicariance events congruent with the Central Highlands Vicariance Hypothesis as well as separate, possibly subsequent, dispersal events. Overall, results of this study corroborate previous evidence for a complex biogeographic history of taxa endemic to rivers of the Central Highlands ecoregion. The improved resolution of genomic variation among studfish populations will guide future studies of morphological variation and will improve conservation plans for rare and endemic taxa in a freshwater biodiversity hotspot.

Unraveling the Evolutionary Patterns of Genus Frontonia: An Integrative Approach with Morphological and Molecular Data

Ciliates of the genus Frontonia have been extensively studied to resolve their phylogenetic and evolutionary history, but challenges remain. This study used molecular analyses of SSU rRNA genes, phylogenetic tree reconstruction, molecular dating, and diversification analysis, together with ancestral state reconstruction of morphological traits and habitat preferences. Data included newly sequenced Korean species, GenBank records and published morphological information. Phylogenetic trees revealed paraphyly within Frontonia, identifying four groups that emerged in the Mesozoic era: Group I (~172 mya), Group II (~83 mya), Group III (~115 mya), and Group IV (~190 mya), with a common ancestor dating to ~420 mya in the Palaeozoic era. Diversification analysis revealed higher extinction rates (0.826 and 0.613 species/year) than speciation rates (0.011 and 0.016 species/year). Morphological evolution showed habitat adaptation and plasticity, with habitat transitions unrelated to contractile vacuolar traits. The SSU rRNA gene polymorphism likely contributed to the paraphyletic state of Frontonia. These results highlight the complex evolutionary patterns of the genus, shaped by genetic diversity, morphology, and environmental constraints.

Flax domesticationprocesses as inferred from genome-wide SNP data

Flax (Linum usitatissimum L.) is one of the founder crops domesticated for oil and fiber uses in the Near-Eastern Fertile Crescent, but its domestication history remains largely elusive. Genetic inferences so far have expanded our knowledge in several aspects of flax domestication such as the wild progenitor, the first use of domesticated flax, and domestication events. However, little is known about flax domestication processes involving multiple domestication events. This study applied genotyping-by-sequencing to infer flax domestication processes. Ninety-three Linum samples representing four flax domestication groups (oilseed, fiber, winter and capsular dehiscence) and its wild progenitor (or pale flax; L. bienne Mill.) were sequenced. SNP calling identified 16,998 SNPs that were widely distributed across 15 flax chromosomes. Diversity analysis found that pale flax had the largest nucleotide diversity, followed by indehiscent, winter, oilseed and fiber cultivated flax. Pale flax seemed to be under population contraction, while the other four domestication groups were under population expansion after bottleneck. Demographic inferences showed that five Linum groups carried clear genetic signals of multiple mixture events that were associated largely with oilseed flax. Phylogenetic analysis revealed that oilseed, fiber and winter flax formed two separate phylogenetic subclades. One subclade had abundant winter flax, along with some oilseed and fiber flax, mainly originating in the Near East and nearby regions. The other subclade mainly had oilseed and fiber flax originating from Europe and other parts of the world. Dating genetic divergences with an assumption of 10,000 years before present (BP) of flax domestication revealed that oilseed and fiber flax spread to Europe 5800 years BP and domestication for winter hardiness occurred in the Near East 5100 years BP. These findings provide new significant insights into flax domestication processes.