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PubMed2026

Mitogenome assembly and phylogenetic relationships of Phalaris arundinacea.

INTRODUCTION: As a perennial herb of Poaceae, Phalaris arundinacea plays key roles in grazing, production, and soil and water conservation because of its well-developed rhizomes and seed dispersal. We assembled and annotated the first mitogenome of P. arundinacea to support evolutionary and taxonomic research. METHODS: We assembled and annotated the first complete mitochondrial genome of P. arundinacea by integrating Illumina short reads with Nanopore long reads via a hybrid assembly strategy. The genome architecture was comprehensively characterized, encompassing codon usage bias, repetitive sequence organization, and inter-organellar genetic exchange with the chloroplast genome. RESULTS AND DISCUSSION: Assembly of the P. arundinacea mitogenome revealed two circular structures with a combined length of 526,717 bp. The genome comprised a set of 37 protein-coding genes (PCGs), 27 tRNAs, and 8 rRNAs, with the rRNA genes exhibiting full assembly (100% coverage). The mitochondrial genome contained 154 forward and 164 palindromic repeats, along with 25 tandem repeats and 124 simple sequence repeats (SSRs). Notably, 102 SSRs were distributed on contig1, predominantly in tetrameric form. Furthermore, 376 RNA editing sites were predicted. A total of 104 fragments were integrated into the mitochondrial genome from the chloroplast, amounting to 55,866 bp of transferred sequence. Finally, phylogenetic analysis of 28 plant mitogenomes placed P. arundinacea closest to species within the genus Poa (P. chaixii and P. pratensis). Comparative analysis of non-synonymous-to-synonymous substitution rate (Ka/Ks) ratios across divergent species revealed that the mitochondrial genome of P. arundinacea underwent stabilizing evolutionary dynamics, characterized by predominant purifying selection with several lineage-specific variations in selective pressure. Our findings support the close phylogenetic relationship between P. arundinacea and species of the genus Poa and provide a reference mitochondrial genome resource for future comparative studies within Phalaris that incorporate broader taxon sampling. These results support deeper phylogenetic investigations of P. arundinacea and facilitate future work on its germplasm characterization and applied use.

Phalaris arundinacea↗

PubMed2026

Phylogenetic position of the enigmatic starfish family Podosphaerasteridae (Asteroidea, Valvatida) with a morphological observation of the skeletal structure by micro-CT.

Background The genus Podosphaeraster comprises seven species, characterised by a distinctive spherical body, all currently known from the seabed at depths below approximately 70 m. Its peculiar morphology has made its phylogenetic placement a subject of ongoing debate. It was initially suggested to be placed in Sphaerasteridae, the same family as fossil species. However, subsequent detailed skeletal analyses of the fossil forms suggested that this similarity was likely due to convergent evolution. Recent molecular analyses have revealed that Valvatida, in which the genus is currently placed, is likely a large polyphyletic group, leaving its taxonomic position still unresolved. New information A detailed examination of the internal skeletal structure of Podosphaeraster toyoshiomaruae, collected from the seas around Japan, was conducted using micro-focus X-ray computed tomography. Concurrently, shotgun sequencing was performed to identify key molecular markers for recent asteroid phylogeny. Additionally, shotgun sequencing determined the complete mitochondrial genome. Despite conservative evolution amongst asteroidean mitochondrial genomes, a translocation of the COX2 gene was revealed, representing the first discovery of a major protein-coding gene translocation within Asteroidea. In the phylogenetic tree, P. toyoshiomaruae was positioned as the most basal lineage within Valvatida. However, the statistical support for this placement was low, potentially due to the long-branch attraction caused by the excessively rapid evolutionary rate. Images reconstructed by micro-CT confirmed the presence of calcified reinforcement in the mesentery and showed its detailed structure for the first time. The mesentery skeleton was found to connect to the V-plate and five pairs of plates, including three kinds of marginal plates. This suggests that the marginal plates of this species may not be homologous with those of other asteroids. Although varying degrees of marginal plate reduction are shared with the order Velatida, we consider this to be a case of convergent evolution. Our phylogenetic analysis indicates a close relationship between P. toyoshiomaruae and Poraniidae (and other Valvatida), all of which possess marginal plates differentiated to varying extents, the homology of which remains uncertain.

Asteroidea↗

PubMed2026

The first two complete mitochondrial genomes for the genus Neotrichoporoides (Hymenoptera, Eulophidae) and their phylogenetic analysis.

Neotrichoporoides belongs to the family Eulophidae (Hymenoptera: Chalcidoidea). As a group of parasitic wasps, it plays an indispensable role in the biological control of agricultural and forest pests and in maintaining ecosystem balance. To date, only nine complete mitochondrial genomes of Eulophidae have been sequenced worldwide, including the two newly sequenced species in this study. To enrich our understanding of the mitochondrial genomic diversity of Eulophidae and to provide preliminary insights into its phylogenetic relationships, we sequenced and comparatively analyzed the mitochondrial genomes of two Neotrichoporoides species. The mitogenomes of N. nyemitawus (GenBank: PZ188956; 15,164 bp) and N. viridimaculatus (GenBank: PX794932; 15,297 bp) contain 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR), and exhibit a strong AT bias, with AT contents of 85.5% and 85.0%, respectively. We further analyzed mitochondrial gene rearrangements across 17 species from Encyrtidae, Eulophidae and Pteromalidae and summarized family-specific rearrangement characteristics. tRNA rearrangements were detected in all three families. Eulophidae harbors conserved PCGs, while the inverse transposition of trnA and transposition of trnV are likely reported for the first time within this family. The two Neotrichoporoides species differ only in the arrangement of several tRNAs. Comparative analysis of PCGs revealed differences in molecular evolutionary rates among genes, with ATP8, ND2 and ND4 evolving faster than the others. Phylogenetic analysis based on mitochondrial genome sequences showed that species from two subfamilies formed a monophyletic group, and congeneric species clustered into a single clade. This study contributes to resolving phylogenetic relationships within Eulophidae and further deepens our understanding of this family.

Eulophidae↗

PubMed2026

The complete chloroplast genome sequence and phylogenetic position of Mallotus apelta.

Mallotus apelta is a perennial species of Euphorbiaceae widely distributed in subtropical East and Southeast Asia. In this study, we sequenced and analyzed its complete chloroplast genome. The genome was 164,055 bp in length and exhibited a typical quadripartite structure, comprising an LSC region of 88,899 bp, an SSC region of 18,494 bp, and two IR regions of 28,331 bp each. A total of 124 genes were annotated. Comparative analyses revealed conserved genome organization and IR boundaries among Mallotus species. Phylogenetic analysis showed that M. apelta was closely related to M. paniculatus, providing valuable resources for Mallotus phylogenetic studies.

Euphorbiaceae↗

PubMed2025

Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance.

Human parainfluenza virus 2 (HPIV-2) and human parainfluenza virus 4 (HPIV-4) are significant but underappreciated respiratory pathogens, particularly among high-risk populations including children, the elderly, and immunocompromised individuals. In this study, we sequenced 101 HPIV-2 and HPIV-4 genomes from respiratory samples collected in western Washington State and performed comprehensive evolutionary analyses using both new and publicly available sequences. Phylogenetic and phylodynamic analyses revealed that both HPIV-2 and HPIV-4 evolve at significantly faster rates compared to the mumps virus, a reference human orthorubulavirus. Notably, while HPIV-2 demonstrated the highest evolutionary rates in the surface glycoprotein HN, consistent with humoral immune-driven selection, the innate immune antagonist V/P gene evolved fastest in HPIV-4. We identified a hypervariable region within the HPIV-4V/P protein (residues 35 to 75), which structural modeling placed in a loop overlapping a known interferon antagonism domain in other paramyxovirus V proteins, though HPIV-4 is functionally incompetent in this activity. Expanded phylogenetic analysis across the Paramyxoviridae family uncovered a striking evolutionary discordance: while the HN glycoprotein and L polymerase of HPIV-4 and its 2 closest bat-derived viruses clustered within the Orthorubulavirus genus, their nucleoprotein (N), phosphoprotein (P), matrix (M), and fusion (F) proteins formed a distinct lineage outside the Rubulavirinae subfamily. Together, these findings highlight the distinct evolutionary trajectories of HPIV-2 and HPIV-4, raise hypotheses around complex Paramyxoviridae zoonotic events including recombination-like patterns, and demonstrate limitations of current L protein-based taxonomic classification schemes.

Humans↗

PubMed2026

Strong phylogenetic signal from chloroplast genomes of three Barringtonia species provides the first genomic resources for their conservation.

BACKGROUND: The genus Barringtonia (Lecythidaceae) is a vital component of tropical coastal forests and mangrove ecosystems. Among its members, B. racemosa and B. fusicarpa are classified as Endangered and Vulnerable, respectively, due to habitat degradation and anthropogenic pressures, underscoring the urgent need for genetic studies to guide conservation. Chloroplast (cp.) genomes serve as essential resources for phylogenetic reconstruction and conservation genetics. However, the scarcity of cp. genome data for Barringtonia has limited comprehensive evolutionary and conservation-oriented investigations. RESULTS: We assembled and annotated the first complete cp. genomes of B. racemosa, B. fusicarpa, and B. acutangula. All three genomes exhibit the typical quadripartite structure, ranging from 158,959 bp (B. racemosa) to 159,837 bp (B. acutangula), and contain 132 genes (87 protein-coding, 37 tRNA, 8 rRNA) with a GC content of 36.68%-36.86%. Collinearity and IR boundary analyses revealed high structural conservation without large-scale rearrangements. Interspecific sequence-level variations were detected in simple sequence repeats (SSRs) and long repeats. Nucleotide diversity (π) analysis identified highly polymorphic regions, including rpl20 (π = 0.080), rpoA (π = 0.064), rps3 (π = 0.063), and ndhF (π = 0.060), which represent promising molecular markers for population genetics within the genus. Codon-based selection analyses (Ka/Ks) showed that all protein-coding genes are under strong purifying selection (mean Ka/Ks 0.32-0.37), with no evidence of positive selection. Pairwise genetic distances (p-distances) among Barringtonia species are extremely low (mean 0.0046), while distances to the related genus Bertholletia are ~ 6-fold higher, supporting their generic distinction. CONCLUSIONS: Phylogenetic analysis robustly supports Barringtonia as a monophyletic clade (bootstrap = 100%), with B. racemosa and B. fusicarpa forming a sister lineage to B. acutangula. This study provides the first high-quality cp. genome resources for the two threatened Barringtonia species, revealing strong structural and sequence conservation but no direct chloroplast genomic correlates of endangerment. The identified polymorphic regions and repeat markers lay a foundation for future population genetics, phylogeographic studies, and conservation-oriented genetic management of these ecologically important coastal plants.

Genome, Chloroplast↗

PubMed2026

Insights into phylogenetic relationships of Veronica species (Plantaginaceae) based on comparative chloroplast genomics.

INTRODUCTION: Veronica L. is one of the most species-rich genera in Plantaginaceae and several species have medicinal, horticultural, or ecological value. METHODS: In this study, the complete chloroplast genomes of three Veronica species were assembled and annotated using Illumina sequencing data. RESULTS: The plastomes exhibited a typical quadripartite structures, with total lengths of 150,202 bp for Veronica biloba L., 151,159 bp for Veronica ciliata Fisch. and 151,098 bp for Veronica vandellioides Maxim. Each genome contained 130-132 unique genes, including 86-87 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analyses of 24 Veronica plastomes indicated that the IR/SC junctions were largely conserved, although slight boundary shifts occurred around rps19, ndhF, and ycf1. Forward, palindromic, complement, and reverse repeats were detected, and A/T mononucleotide repeats were the dominant SSR type. Nucleotide diversity analysis identified rpl32-trnL, trnK-rps16, rpl32, ycf1, ndhF, accD, matK, and rpoB as highly variable regions. Phylogenetic analyses recovered Veronica as a well-supported monophyletic lineage and clarified the plastid positions of the three newly sequenced species. Divergence time estimation suggested that the estimation suggested of Veronica was around 14.9 Ma, with V. biloba, V. ciliata and V. vandellioides diverging approximately 3.9 Ma, 0.6 Ma, and 6.9 Ma, respectively. DISCUSSION: Because the analyses were based on plastid genomes, the inferred topology should be interpreted as chloroplast phylogenetic evidence rather than a complete species-history reconstruction. These results provide plastome resources and molecular evidence for taxonomy, species identification, and future evolutionary studies of Veronica.

Plantaginaceae↗

PubMed2026

A New Species of Eucnemidae (Coleoptera: Elateroidea) with Its Complete Mitogenome and Mitogenome-Based Phylogenetic Analysis.

We describe Microrhagus ziwulingensis Muona & Meng, sp. nov., from China. The genus Microrhagus Dejean, 1833, was previously represented in China by only two species. We sequenced and assembled the complete mitogenome of M. ziwulingensis (GenBank accession OK143440), which encoded 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a putative control region with a total length of 15,843 bp. Overall, 36 species of Elateroidea were collected as the ingroup (for six of these species, two sequences of the same species submitted by different submitters were used). Eight species of Buprestoidea served as the outgroup. We constructed phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) methods based on 13 protein-coding genes (PCGs) from mitochondrial genomes. The phylogenetic trees showed that all families within the superfamily Elateroidea, which was used as the ingroup, formed monophyletic groups. The topology differed from previous studies, showing that Rhagophthalmidae and Lampyridae formed a sister clade, and that Phengodidae + Lycidae, with Cantharidae, formed a sister clade. These discrepancies should be attributed to the use of a single type of molecular marker and the intense shortage of available sampling. This also indicates that mitochondrial genomic research on Eucnemidae, and even on the superfamily Elateroidea, still needs further expansion.

Microrhagus↗

PubMed2025

Phylogenetic and Genetic Evolution Analysis of Complete SFTSV Genome Sequences in Shandong Province, China.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by SFTS virus (SFTSV). Shandong province is one of the epidemic regions with high incidence rate of SFTS. To investigate phylogenetical and genetic evolution characteristics of SFTSV in Shandong province, we isolated SFTSV from suspected patients between April 2023 and October 2024, and then whole SFTSV genomes were amplified and sequenced in this study. A total of 25 new strains were analyzed together 56 strains submitted in Genbank from Shandong province. Phylogenetical and genetic analyses of the data set revealed that four genotypes were co-circulating in Shandong province. C3 genotype was the most common genotype in each year with lower genetic divergence. 298 amino acid substitutions were detected in the four proteins of SFTSV, but only two substitutions (Arg624Lys and Arg962Ser) had been proven to have potential impacts on biological functions. In addition, one reassortment strain (C3/C4/C4 for L, M and S segments) and three recombinant strains were identified. Analysis of selection pressure at the level of amino acid substitutions indicated genes within the four ORFs of SFTSV were all subjected to negative selection. In conclusion, the genetic characteristics and evolutionary mechanism of SFTSV was complex in Shandong province. It is necessary to conduct continuous surveillance to grasp the genetic evolution patterns, and to discover novel prevalent variants in a timely manner.

China↗

PubMed2026

Comparison of phylogenetic metrics of transmission between symptomatic and asymptomatic tuberculosis in individuals who were incarcerated in Brazil in 2008-24: a retrospective genomic epidemiology study.

BACKGROUND: Tuberculosis control efforts have traditionally targeted symptomatic individuals; however, the role of asymptomatic cases in sustaining transmission is increasingly recognised. We aimed to quantify the contribution of asymptomatic tuberculosis to recent transmission using genomic and epidemiological data from a high-transmission setting. METHODS: We conducted a retrospective genomic epidemiology study of Mycobacterium tuberculosis isolates collected in Mato Grosso do Sul, Brazil, between Aug 25, 2008, and March 19, 2024. Available isolates underwent whole-genome sequencing. Demographic, clinical, incarceration history, and laboratory metadata were obtained from surveillance records. From Jan 1, 2017, to March 19, 2024, active case finding was conducted in the state's three largest prisons (all male-only facilities), during which sputum samples were collected from individuals irrespective of symptoms and tested using GeneXpert and culture. Comparisons of transmission between individuals with and without symptoms were restricted to individuals who were incarcerated and were identified through active case finding and for whom high-quality, M tuberculosis lineage 4 genomes were available. Metrics of recent transmission included phylogenetic clustering, time-scaled haplotype density (THD), local branching index (LBI), and transmission probabilities inferred using Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories. FINDINGS: 4448 tuberculosis cases were notified in Mato Grosso do Sul in 2008-24. After excluding cases for which M tuberculosis isolates were not available or had low sequencing quality, who had contaminated cultures or mixed infection, or who were infected with non-lineage 4 M tuberculosis, we included 2362 lineage 4 M tuberculosis isolates with high-quality genome sequences. 1849 (78·3%) of 2362 isolates were part of a genomic cluster. Among 2362 individuals with tuberculosis, 1137 (48·1%) were incarcerated at diagnosis. Of these individuals, 505 were identified through active case finding in three male-only prisons. The median age was 30 years (IQR 25-37); 304 (60·2%) had mixed ethnicity, 90 (17·8%) were White, 56 (11·1%) were Black, 13 (2·6%) were Indigenous, and six (1·2%) were Asian. 277 (54·9%) had symptomatic disease and 228 (45·1%) had asymptomatic tuberculosis. There were no significant differences between symptomatic and asymptomatic individuals in phylogenetic clustering (213 [76·9%] of 277 vs 195 [85·5%] of 228; p=0·37), THD (median 0·39 [IQR 0·06-0·62] vs 0·50 [0·09-0·65]; p=0·12), or LBI (0·00863 [0·00810-0·00988] vs 0·00871 [0·00829-0·01020]; p=0·088). Bayesian transmission trees showed no significant difference in the number of secondary infections inferred from symptomatic compared with asymptomatic individuals (p=0·56). These findings were consistent across genomic clusters and robust to model assumptions. INTERPRETATION: We identified no differences in transmission between individuals who were symptomatic and those who were asymptomatic using multiple genomic measures. In this high-transmission setting, where systematic screening is implemented, our findings indicate that asymptomatic tuberculosis substantially contributes to tuberculosis transmission at the population level. These results suggest that symptom-based case detection alone is likely to be insufficient to interrupt transmission and highlight the importance of expanded screening strategies in high-risk populations. FUNDING: US National Institutes of Health and the Brazilian National Research Council (CNPq).

Humans↗

PubMed2026

Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy.

Pathogen genomic analysis is central to tracking, understanding and containing outbreaks1-13, but the complexity and cost of state-of-the-art phylogenetic tools limit global access and impact. Here we introduce Delphy, an exact reformulation of Bayesian phylogenetics14-17 designed to transform its speed, scalability and accessibility while retaining Bayesian state-of-the-art accuracy. Delphy's central data structure, an explicit mutation-annotated tree, takes advantage of the high sequence similarity of large-scale epidemic datasets18-20 for efficient tree exploration and convergence. By reproducing key analyses from recent major epidemics, including Ebola1,21, Zika2, SARS-CoV-2 (ref. 22), mpox3,4 and H5N1 (refs. 23,24), we demonstrate state-of-the-art accuracy with up to 2-3 orders of magnitude improvements in speed. Assessing Delphy's scalability, we show that a simulated dataset of 100,000 sequences can be analysed within a day. We distribute Delphy as a client-side web application that enables local, interactive analysis of raw data on the user's machine. Delphy automatically identifies key viral lineages and mutations, as well as their emergence and prevalence through time, with quantified uncertainties grounded in Bayesian theory. Delphy establishes Bayesian phylogenetics as a fast, accessible frontline tool for future outbreak response.

Journal Article↗

PubMed2026

SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.

MOTIVATION: Phylogenetic networks represent complex biological scenarios that are overlooked in trees, such as hybridization and horizontal gene transfer. Although numerous methods have been developed for phylogenetic network inference, their scalability is severely limited by the computational demands of likelihood optimization and the vastness of network space. Composite (or pseudo-) likelihood approaches like SNaQ have improved computational tractability for network inference, but they remain inadequate for datasets of sizes routinely handled by tree inference methods. RESULTS: Here, we introduce SNaQ.jl, a new standalone Julia package with the composite likelihood inference originally implemented within PhyloNetworks.jl as well as new scalability features that enhance computational efficiency through (i) parallelization of quartet likelihood calculations during composite likelihood computation, (ii) weighted random selection of quartets, and (iii) probabilistic decision-making during network search. Through a simulation study and empirical data analysis, we show that this new version of SNaQ.jl (version 1.1) improves average runtimes by up to 499% on average with no change in function parameters or method accuracy. AVAILABILITY AND IMPLEMENTATION: SNaQ.jl is a new open source Julia package available at https://github.com/JuliaPhylo/SNaQ.jl.

Phylogeny↗

PubMed2025

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.

Evolutionary sparse learning uses supervised machine learning to build evolutionary models where genomic sites loci are parameters. It uses the Least Absolute Shrinkage and Selection Operator with bi-level sparsity to connect a specific phylogenetic hypothesis with sequence variation across genomic loci. The MyESL software addresses the need for open-source tools to perform evolutionary sparse learning analyses, offering features to preprocess input phylogenomic alignments, post-process output models to generate molecular evolutionary metrics, and make Least Absolute Shrinkage and Selection Operator regression adaptable and efficient for phylogenetic trees and alignments. The core of MyESL, which constructs models with logistic regressions using bi-level sparsity, is written in C++. Its input data preprocessing and result post-processing tools are developed in Python. Compared to other tools, MyESL is more computationally efficient and provides evolution-friendly inputs and outputs. These features have already enabled the use of MyESL in two phylogenomic applications, one to identify outlier sequences and fragile clades in inferred phylogenies and another to build genetic models of convergent traits. In addition to the use in a Python environment, MyESL is available as a standalone executable compatible across multiple platforms, which can be directly integrated into scripts and third-party software. The source code, executable, and documentation for MyESL are openly accessible at https://github.com/kumarlabgit/MyESL.

Phylogeny↗

PubMed2025

The distribution of fitness effects varies phylogenetically across animals.

The distribution of fitness effects (DFE) describes the selection coefficients () of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (), and the proportion of new beneficial mutations (). These findings align with Fisher's Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGM's predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals.

Fisher’s geometric model↗

PubMed2025

Comparison of phylogenetic metrics of transmission in symptomatic and asymptomatic tuberculosis.

BACKGROUND: Understanding drivers of Mycobacterium tuberculosis (Mtb) transmission remains a critical challenge in high-burden settings. Tuberculosis control efforts traditionally target symptomatic individuals, yet the role of asymptomatic cases in sustaining transmission is increasing recognized. METHODS: We conducted a genomic and epidemiological analysis of Mtb isolates collected in Mato Grosso do Sul, Brazil, between 2008 and 2024. From 2017 to 2022, active case finding was performed in three of the state's largest prisons, whereby sputum was collected from individuals irrespective of symptoms and tested by GeneXpert and culture. We evaluated several metrics of recent transmission from symptomatic and asymptomatic individuals, including phylogenetic clustering, Time-scaled Haplotype Density (THD), Local Branching Index (LBI), and transmission probabilities inferred using the Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH). FINDINGS: We sequenced 2,362 Mtb strains, of which 3.5% (115/2,362) were resistant to at least one drug, and 0.6% (16/2,362) were multi-drug resistant. Most strains were lineage 4, and 78.2% of all isolates were part of a genomic cluster. Among 2,362 individuals with tuberculosis, 1,137 were incarcerated at the time of diagnosis. Among these, 505 were identified through active case finding: 277 had symptomatic disease and 228 had asymptomatic tuberculosis. There was no significant difference in phylogenetic clustering proportion (77% vs. 85%; p= 0.816), THD (median 0.50 vs. 0.39; p = 0.120), or LBI (median 0.00863 vs. 0.00871; p = 0.086) between symptomatic and asymptomatic individuals. Bayesian transmission trees revealed no significant difference in the number of secondary infections inferred from symptomatic compared with asymptomatic individuals (p = 0.56). These findings were consistent across genomic clusters and robust to model assumptions. INTERPRETATION: We identified no differences in transmission from symptomatic compared with asymptomatic individuals, using several genomic measures of transmission, underscoring the substantial contribution that asymptomatic tuberculosis makes to transmission at the population level.

Asymptomatic↗

PubMed2026

Target Capture of Ancient Shell DNA Enables Phylogenetic Reconstruction of Deep-Sea Molluscs.

Target capture is widely used to enrich endogenous DNA from calcium phosphate skeletal material in vertebrates, but its performance on calcium carbonate hard parts widely produced by invertebrates remains poorly understood. Here, we compared DNA recovery from four fresh and 12 ancient (eight radiocarbon-dated to 1671-1135 years old before present) deep-sea vesicomyid clam shells, including species Archivesica marissinica, A. nanshaensis and A. okutanii, using whole-genome sequencing (WGS) or target capture of ultraconserved elements (UCEs). WGS achieved 16.65% on-target read recovery of UCEs from fresh soft tissue, but < 1% from shell specimens. By contrast, UCE capture in the same specimen increased on-target reads by up to 155-fold, reaching 29.84% in fresh shells and up to 72-fold, reaching 19.89% in ancient shells. Target capture of UCEs recovered 142-1001 loci per sample compared to 0-230 with WGS alone. Ancient shells of A. marissinica and A. okutanii, based on reads mapped with bwa-mem2 and bbmap, exhibited characteristic post-mortem DNA damage signals, with average 5'-end C-to-T misincorporation rates of 3.46% and 15.97%, respectively, exceeding the levels observed in fresh A. marissinica shells (maximum 1.24%). UCE-based phylogenetic reconstructions incorporating shell ancient DNA recovered two major clades within Pliocardiinae, consistent with published phylogenomic trees. Together, these findings demonstrate that target-capture enrichment enables effective recovery of highly degraded DNA from ancient mollusc shells and supports robust phylogenetic inference at the intrageneric scale, expanding the utility of shells-one of the most abundant invertebrate remains-for evolutionary, biogeographic and conservation studies.

Animals↗

PubMed2025

Whole genome sequencing and phylogenetic classification accelerate the implementation of respiratory syncytial virus genomic surveillance in Canada: a pilot study.

UNLABELLED: Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens, including respiratory syncytial virus (RSV). Multiplex tiling polymerase chain reaction (PCR) assays have been used to facilitate sequencing of a variety of pathogens in support of genomics-based surveillance initiatives. We developed, optimized, and implemented multiplex tiling PCR assays for RSVA and RSVB capable of generating near-complete genomes in the majority of contemporaneous specimens tested. A pilot data set comprising 52 RSVA and 37 RSVB genomes derived from Canadian clinical specimens during the 2022-2023 respiratory virus season was used to perform phylogenetic analyses using both near-complete genome and glycoprotein (G) sequences. Overall, the RSV phylogenetic tree built with whole genomes showed identical lineage clusters as compared to the G gene but was more discriminatory. Moreover, the availability of complete genomes enables the identification of a broader range of mutations. For instance, mutations identified in the fusion protein among Canadian isolates tested here, including S377N, K272M, S276N, S211N, S206I, and S209Q, could affect the efficacy of current vaccines or antiviral-based therapeutics. In conclusion, our work reinforces other recent studies demonstrating the utility of multiplex tiling PCR assays to facilitate high-throughput WGS of RSV, which is capable of supporting enhanced genomic surveillance initiatives, as well as the more comprehensive genomic analyses required to inform public health strategies for the development and usage of vaccines and antiviral drugs. IMPORTANCE: We present assays to efficiently sequence genomes of RSVA and RSVB. This enables researchers and public health agencies to acquire high-quality genomic data using rapid and cost-effective approaches. Genomic data-based comparative analysis can be used to conduct surveillance and monitor circulating isolates for efficacy of vaccines and antiviral therapeutics.

Humans↗

PubMed2026

Detection and phylogenetic characterization of Jingmen tick virus in Amblyomma mixtum ticks from Costa Rica.

UNLABELLED: Jingmenviruses are a group of segmented flaviviruses detected in arthropods and vertebrates that have attracted growing public health interest due to the recognition of some members as emerging human arboviral pathogens. As part of a study aimed at deciphering the virome of ticks of medical and veterinary importance in Costa Rica, we detected Jingmen tick virus (JMTV) in host-feeding Amblyomma mixtum ticks collected from horses. We assembled three complete genome segments and one partial segment from tick pools. Phylogenetic analyses revealed that JMTV from Costa Rica (JMTV Costa Rica) shares a common viral ancestor with JMTV viruses identified in ticks from the Caribbean and Latin America. Two distinct clades of Jingmenviruses were identified in the American continent, suggesting two distinct introductions: one from Europe/Asia and the other from Africa/Asia. Of note, JMTV Costa Rica falls in the same clade as viruses from Europe and Western Asia, including sequences found in humans. Our study constitutes the first detection of JMTV in Amblyomma mixtum. This tick species feeds on a wide range of hosts, including wildlife, domestic animals, and frequently parasitizes humans in Central America. Further research involving the detection of active and past infections by JMTV in humans and horses after tick bites is needed to evaluate the risk of spillover in Central America, including Costa Rica. IMPORTANCE: Jingmenviruses are flaviviruses detected in arthropods and vertebrates, reported in several countries worldwide. Some members cause disease and infections in humans; therefore, they are considered emergent human arboviruses. In Costa Rica and Central America, there is no information on tick-associated viruses or the role of ticks as putative vectors of viruses. Here, we report the first regional detection of Jingmen tick virus (JMTV) in Amblyomma mixtum ticks collected from horses. We assembled three complete and one partial viral segment from tick pools. Phylogenetic analysis revealed that the JMTV detected in Costa Rica is closely related to other detections from Latin America and the Caribbean and is located in the same clade as viruses reported in humans. Additionally, we detected two separate introductions of JMTV to Latin America. To determine whether this JMTV is an emergent arbovirus locally, research on past or active infections in humans is required.

Animals↗