SEARCH · Search PubMed

Results for “Phylogenetic inference”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2026

Can't see the forest for the trees: The influence of marker type on inferred phylogenetic relationships in a cosmopolitan bat genus.

Fine-resolution information on species relationships and biological diversity is critically needed to guide conservation efforts amidst rapid environmental changes. Systematics, which forms the foundation of this knowledge, has been revolutionized by phylogenomics, utilizing genome-scale datasets. However, the use of diverse marker types, non-comparable taxon sampling, and outgroup selection can lead to conflicting phylogenetic hypotheses. These inconsistencies complicate study comparisons and hinder our ability to assess marker-specific impacts on phylogenetic resolution. The phylogenetic reconstruction of the bat genus Myotis, encompassing over 140 species and characterized by a rapid radiation in the last 20 million years, has been particularly influenced by these challenges. Achieving phylogenetic resolution in Myotis is particularly complex due to subtle interspecific differences in both morphological and molecular traits. Mitochondrial and nuclear markers often produce discordant trees, influenced by hybridization, introgression, and methodological variations. In this study, we employed a consistent taxonomic sample set of 44 Myotis taxa to evaluate the impact of five different genetic marker types on phylogenetic reconstruction. We observed significant discordance between topologies derived from conserved nuclear and mitochondrial markers and found that transposable elements were inadequate for resolving relationships across the entire genus. Our results also clarify the placement of previously problematic taxa within the genus. These findings emphasize the importance of aligning genetic marker choice with specific phylogenetic questions and highlight the influence of taxonomic and methodological variation on phylogenomic outcomes. This work provides a framework for improving phylogenetic inference in rapidly radiating groups and enhances our understanding of evolutionary history in Myotis.

Animals↗

PubMed2026

Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice.

Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

Phylogeny↗

PubMed2026

IQ-NET: fast and accurate quartet phylogenetic inference using deep learning trained on empirical DNA alignments.

Phylogenetic inference is fundamental to modern biology, with many applications including evolutionary biology, epidemiology, and comparative genomics. While maximum likelihood and Bayesian methods remain the gold standard for phylogenetic analysis, they rely on simplifying assumptions and are computationally intensive. Recent machine learning approaches for phylogenetics offer speed advantages, but have several limitations: exclusive reliance on simulated data for training, inadequate handling of gaps, and sensitivity to input sequence order. Here, we introduce IQ-NET (Intelligent Quartet NETwork), a deep learning framework that solves these limitations to infer four-taxon trees. IQ-NET estimates both tree topology and branch lengths directly from gapped alignments. IQ-NET outperforms existing machine learning methods in terms of accuracy, and obtained a 24-fold speedup compared with the widely used maximum likelihood software, IQ-TREE. We finally introduce a pipeline using IQ-NET and the ASTRAL software to reconstruct a larger species tree, i.e., with more than four taxa.

Empirical data training↗

PubMed2025

Parallel algorithms for phylogenetic inference under a structured coalescent approximation.

While advances in molecular epidemiology and computational modeling have enhanced our capacity to track pathogen evolution, the accurate reconstruction of spatiotemporal transmission dynamics remains essential for developing epidemic preparedness frameworks and implementing outbreak response measures. Structured coalescent models offer a phylogeographic framework by restricting lineage coalescence events to geographically proximate host populations. Although the Bayesian structured coalescent approximation (BASTA) provides a tractable approach, contemporary phylogeographic analyses involving dozens of geographic localities and hundreds to thousands of viral genomes substantially exceed the computational capacity of existing implementations. The BASTA likelihood scales cubically with deme count and quadratically with sequence count due to matrix exponentiation and pairwise coalescent probability calculations. Here, we introduce a comprehensive algorithmic restructuring of the structured coalescent likelihood that eliminates redundancies, optimizes memory access, and exposes parallelization opportunities. Our approach reorganizes computations along three dimensions: (i) independent calculation of deme-transition probability matrices across time intervals; (ii) simultaneous evaluation of partial likelihood vectors within temporal slices; and (iii) concurrent aggregation of coalescent probabilities. Algorithmic restructuring cuts average coalescent likelihood computation by 7-8 fold, and parallelization further boosts performance to 10-26 fold, enabling joint phylogeographic analyses of dengue virus across 10 South American countries and H5N1 avian influenza across 20 Eurasian regions to finish in a fraction of prior time. This computational efficiency also enables comparison between backward-in-time structured coalescent approximations and forward-in-time phylogeographic methods, revealing that the former provides appropriately conservative posterior estimates, particularly at intermediate phylogenetic depths. We integrate our implementation into the popular BEAST X and BEAGLE software packages, with an accompanying interface in BEAUti X to easily set up the analyses, providing researchers with an accessible and scalable tool for real-time phylogeographic surveillance of rapidly evolving pathogens.

Journal Article↗

PubMed2026

Bit-reproducible parallel phylogenetic tree inference.

MOTIVATION: Phylogenetic trees describe the evolutionary history among biological species based on their genomic data. Maximum likelihood (ML) based phylogenetic inference tools search for the tree and evolutionary model that best explain the observed genomic data. Given the independence of likelihood score calculations between different genomic sites, parallel computation is commonly deployed. This is followed by a parallel summation over the per-site scores to obtain the overall likelihood score of the tree. However, basic arithmetic operations on IEEE 754 floating-point numbers, such as addition and multiplication, inherently introduce rounding errors. Consequently, the order by which floating-point operations are executed affects the exact resulting likelihood value since these operations are not associative. Moreover, parallel reduction algorithms in numerical codes re-associate operations as a function of the core count and cluster network topology, inducing different round-off errors. These low-level deviations can cause heuristic searches to diverge and induce high-level result discrepancies (e.g. yield topologically distinct phylogenies). This effect has also been observed in multiple scientific fields beyond phylogenetics. RESULTS: We observe that varying the degree of parallelism results in diverging phylogenetic tree searches (high-level results) for over 31% out of 10 179 empirical datasets. More importantly, 8% of these diverging datasets yield trees that are statistically significantly worse than the best-known ML tree for the dataset (AU-test, P < .05). To alleviate this, we develop a variant of the widely used phylogenetic inference tool RAxML-NG, which does yield bit-reproducible results under varying core-counts, with a slowdown of only 0%-12.7% (median 0.8%) on up to 768 cores. For this, we introduce the ReproRed reduction algorithm, which yields bit-identical results under varying core-counts, by maintaining a fixed operation order that is independent of the communication pattern. ReproRed is thus applicable to all associative reduction operations-in contrast to competitors, which are confined to summation. Our ReproRed reduction algorithm only exchanges the theoretical minimum number of messages, overlaps communication with computation, and utilizes fast base-cases for local reductions. ReproRed is able to all-reduce (via a subsequent broadcast) 4.1×106 operands across 48-768 cores in 19.7-48.61 μs, thereby exhibiting a slowdown of 13%-93% over a non-reproducible all-reduce algorithm. ReproRed outperforms the state-of-the-art reproducible all-reduction algorithm ReproBLAS (offers summation only) beyond 10 000 elements per core. In summary, we re-assess non-reproducibility in parallel phylogenetic inference, present the first bit-reproducible parallel phylogenetic inference tool, as well as introduce a general algorithm and open-source code for conducting reproducible associative parallel reduction operations. AVAILABILITY AND IMPLEMENTATION: ReproRed: https://doi.org/10.5281/zenodo.15004918 (LGPL)-Reproducible RAxML-NG version https://doi.org/10.5281/zenodo.15017407 (GPL).

Phylogeny↗

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↗

PubMed2023

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.

Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.

Animals↗

PubMed2026

Identification of a novel HIV-1 circulating recombinant form (CRF209_cpx) and its descendant unique recombinant form (URF) CRF209_cpx/B among MSM in Guangdong, southern China.

BACKGROUND: The epidemic of human immunodeficiency virus type 1 (HIV-1) continues to pose a significant global health challenge, with increasing genetic diversity. The co-circulation of multiple subtypes among the local population facilitates the emergence of unique or circulating recombinant forms (URFs or CRFs). In China, the predominant strains include CRF07_BC, CRF01_AE, CRF55_01B, and subtype B. This study characterizes a novel CRF209_cpx and its descendant recombinant CRF209_cpx/B among men who have sex with men (MSM) in Guangdong, southern China. METHODS: Individuals infected with URFs with similar genetic characteristics were recruited during routine surveillance of pretreatment drug resistance. Near full-length genomes (NFLGs) were amplified with two overlapping fragments using a serial dilution nested PCR approach after reverse transcription. We used SimPlot and IQ-TREE softwares to conduct recombination analyses and phylogenetic inferences. Time-scaled maximum clade credibility (MCC) phylogenetic trees were reconstructed using BEAST software to estimate evolutionary origins. Genotypic drug resistance mutations were interpreted via the Stanford HIV Database, and coreceptor usage was predicted using geno2pheno coreceptor 2.5 and the HIVcoPRED tool. RESULTS: Four NFLG sequences were obtained and identified as a novel CRF209_cpx, generated by recombination among CRF01_AE, CRF07_BC and subtype B. Phylogenetic analyses revealed that all the parental segments clustered with lineages prevalent among MSM in China. Bayesian evolutionary analysis estimated that the most recent common ancestor (tMRCA) of CRF209_cpx to have evolved between 2011 and 2013. The fifth strain was identified as a URF recombined from nascent CRF209_cpx and B. No transmitted drug resistance mutation was detected in these five sequences. The four CRF209_cpx sequences primarily utilized the CXCR4 coreceptor, while the URF exhibited R5/X4 dual tropism. CONCLUSIONS: The emergence of the complex CRF209_cpx and novel URF of CRF209_cpx/B highlights the active HIV-1 epidemic within the MSM population in Guangdong, underscoring the necessity for enhanced molecular surveillance and precise public health intervention in this key population.

HIV-1↗

PubMed2026

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys).

Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last 5 million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as "sexual swindling". However, the rapid and substantial diversification of this genus, combined with its capacity for hybridization and large genome size, poses significant challenges in addressing its systematics. We used phylotranscriptomics as a genome complexity reduction technique to infer the phylogenetic relationships among Ophrys main lineages. More than seven thousand gene trees enabled us to determine the relative contributions of gene flow and incomplete lineage sorting (ILS) in Ophrys evolution. First, we propose a new phylogenetic hypothesis for the genus with an unprecedented resolution that largely confirms the relationships between the main Ophrys lineages, but also provides new insights within each subgenera. By combining phylogenetic network inference with introgression analyzes based on gene tree topologies and branch lengths, we then show that the numerous phylogenetic incongruences among gene tree topologies result from a pervasive background of ILS, over which stand out several well-supported, ancient and potentially adaptive gene flow events between lineages. These major gene flow events provide a new perspective on the evolution of the Ophrys genus and its pollination, questioning previous hypotheses inferred without considering its reticulate evolution, and providing a better understanding of discrepancies observed among previous phylogenetic studies of the genus.

Orchidaceae↗

PubMed2026

Assembly and comparative analysis of the mitochondrial genome of Pleione yunnanensis: genome structure and evolutionary insights.

BACKGROUND: Pleione yunnanensis a terrestrial or semi-epiphytic herbaceous plant belonging to the Orchidaceae family, is valued for both its medicinal uses and ornamental appeal. Although its chloroplast genomes have been sequenced, its complete mt genome had not previously been resolved, limiting genetic and evolutionary studies of the species. RESULTS: In this work, we assembled and characterized the first complete mt genome of P. yunnanensis, revealing a structurally complex, multibranched system composed of 14 circular-mapping molecules totaling 468,176 bp with a GC content of 44.32%. The genome encodes 44 annotated genes, including 28 protein-coding genes (PCGs), 15 tRNAs, and one rRNA. The multibranched architecture provides new evidence supporting the dynamic and recombinational nature of plant mt genomes. Repeat analysis uncovered 29 simple sequence repeats (SSRs), 19 tandem repeats, and 118 dispersed repeats, indicating a comparatively lower repeat abundance than that found in closely related orchids with similar mt genome sizes. Codon-usage profiling of PCGs showed a marked bias toward A/T-ending codons. Prediction of RNA editing sites identified 4,708 putative edits across mitochondrial PCGs. Most mitochondrial genes displayed Ka/Ks ratios close to 1.0, suggesting relaxed selective constraints or lineage-specific evolutionary patterns rather than strong positive selection. Moreover, we detected 69 chloroplast-derived homologous fragments, including 15 intact genes, suggesting ongoing plastid-mitochondrial DNA transfer. Phylogenetic reconstruction and collinearity comparisons demonstrated that P. yunnanensis clustered closely with Dendrobium species, including D. amplum and D. hancockii, within the Orchidaceae clade. CONCLUSIONS: This study provides the first complete mt genome of P. yunnanensis, providing a foundational genomic resource for the genus Pleione. The results not only improve our understanding of mt genome structure and evolution in Orchidaceae, but also offer valuable molecular evidence for phylogenetic inference, germplasm identification, and conservation of this endangered medicinal species.

Orchidaceae↗

PubMed2026

First nationwide full-genome characterisation of human-derived Andes virus in Chile: a retrospective genomic epidemiology study.

BACKGROUND: Andes virus (ANDV) is the only hantavirus known to transmit between humans and causes hantavirus cardiopulmonary syndrome in Chile and Argentina. In Chile, ANDV genomic diversity remains incompletely characterised. This study aimed to characterise the genetic diversity, geographical structure, and molecular signatures of ANDV using human clinical samples collected over a 13-year period (2011-24). METHODS: We conducted a retrospective genomic epidemiology study of ANDV infections in Chile. Clinical samples from patients with confirmed ANDV, collected between March 9, 2011, and June 27, 2024, were analysed and sequenced. Clinical and epidemiological data were obtained from diagnostic laboratories and surveillance programmes. Consensus sequences for the S, M, and L segments were generated, and genetic clustering and divergence were assessed using phylogenetic inference and variant calling. FINDINGS: We analysed clinical samples from 58 infected individuals and identified two major genomic variants of ANDV with distinct geographical distributions, defined by regionally structured patterns of nucleotide and amino acid substitutions across the S, M, and L segments: ANDV Chi-North (central Chile) and ANDV-South (southern Chile). No consistent clustering by clinical severity was observed, and no recurrent non-synonymous substitutions were uniquely associated with severe disease. Substitutions previously associated with person-to-person transmission in outbreaks in Argentina were not consistently observed in Chilean sequences, including in four person-to-person transmission cases. Although some substitutions described in ANDV-like viruses were present in the Chi-North lineage, this lineage remained phylogenetically distinct and geographically restricted to central Chile. INTERPRETATION: To our knowledge, this study provides the first nationwide genomic characterisation of human-derived ANDV in Chile. The identification of geographically structured variants indicates that ANDV diversity in Chile is driven by regional diversification rather than clinical outcome. The absence of consistent amino acid signatures associated with disease severity or person-to-person transmission suggests that these phenotypes are unlikely to be explained by viral genetic variation alone. These findings refine current understanding of ANDV evolution and highlight the need for continued integrated genomic surveillance in endemic regions. FUNDING: Agencia Nacional de Investigación y Desarrollo de Chile and National Institutes of Health.

Humans↗

PubMed2027

Global Genomic Surveillance.

Global genomic surveillance has emerged as a foundational pillar of public health in the twenty-first century, enabling real-time tracking of pathogen evolution and informing outbreak response. This chapter examines the strategic architecture of global genomic surveillance, focusing on its application to arboviruses such as chikungunya virus (CHIKV). It explores the integration of genomic data with epidemiological, clinical, and environmental information within a One Health framework, while addressing critical challenges in governance, equity, and interoperability. The discussion covers the entire genomic surveillance workflow, from sample collection and sequencing to bioinformatic analysis and phylogenetic inference, and highlights the transformative role of artificial intelligence (AI) in predictive surveillance. By analyzing global initiatives, operational barriers, and emerging technologies, this chapter underscores the necessity of sustainable, equitable, and interoperable genomic systems to proactively address current and future infectious disease threats.

Humans↗

PubMed2025

Mitochondrial Impostors: Prevalence and Impacts of NUMTs on Genetic and Evolutionary Studies in Carnivora.

Nuclear mitochondrial pseudogenes are mitochondria-derived DNA sequences integrated into the nuclear genome, which can introduce errors in species identification, phylogenetic inference, and population genetics. Although nuclear mitochondrial pseudogene contamination has been reported in some Carnivora species, a systematic investigation into the prevalence and impacts of nuclear mitochondrial pseudogenes across an order is still lacking. In this study, 22,102 mitochondrial DNA sequences of 80 Carnivora species from 14 families and 54 genera were retrieved from the public National Center for Biotechnology Information database and further analyzed. Using alignment-based methods, 158 problematic sequences/sequence groups were identified and categorized into four types: nuclear mitochondrial pseudogenes, species misidentification or mislabeling, sequence errors, and anomalous sites. Among families, Felidae exhibited the highest rate of nuclear mitochondrial pseudogene contamination, particularly in species of the genus Panthera. In contrast, no nuclear mitochondrial pseudogene contamination was detected in members of Ursidae and Ailuridae. Phylogenetic analysis revealed multiple independent origins of nuclear mitochondrial pseudogene, with some tracing back to the common ancestor of Carnivora. To mitigate nuclear mitochondrial pseudogene-related errors, rigorous sequence verification strategies, such as sequence alignment and phylogenetic validation, should be implemented. In conclusion, our findings highlight the necessity of nuclear mitochondrial pseudogene awareness in genetic and evolutionary studies of Carnivora and other taxa.

Animals↗

PubMed2025

Frequent Genomic Recombination in the 5'-Proximal Region Characterizes Human Adenovirus Species C Evolution.

To advance our understanding of the molecular recombination dynamics of circulating human adenovirus species C (HAdV-C) strains, whole genome sequence (WGS) analysis of seven strains representing five genotypes (P1H1F1, P1H2F2, P89H5F5, P2H2F2, and Px1/Ps3H1F1) isolated from pediatric severe acute respiratory infection (SARI) cases in China were performed, involving sequence similarity assessment, phylogenetic inference, and recombination mapping. The genomic analysis of seven strains showed substantial nucleotide identity (93.5%-99.2%) and distinct recombination patterns. Further comparative recombinant analysis with eight prototype strains and 214 publicly available strains revealed that strains with high genomic similarity or evolutionary relatedness showed substantial conservation in the posterior genomic regions, while the 5'-proximal ~14 000 bp region, particularly E1 and E2B regulatory and replication-associated genes, displayed significant recombination activity. In addition, identical or similar recombination patterns were found in the genomes of strains with high sequence identity and homology, which had been detected by different surveillance systems, and in multiple provinces in China and other countries. Further analysis revealed an independent evolutionary cluster for two strains (Henan2018-431 and Jilin2019-101), which also harbored fragments of unknown origin within the E3 region, potentially representing novel HAdV-C variants. These findings highlight the critical role of frequent recombination in HAdV-C evolution, particularly in low-diversity genomic regions, and emphasize the importance of WGS-based surveillance for tracking emerging recombinant strains with public health implications.

Humans↗

PubMed2025

Bayesian Phylogenetic Lineage Reconstruction with Loss of Heterozygosity Mutations Derived from Single-Cell RNA Sequencing.

Mutations are acquired frequently, such t`hat each cell's genome inscribes its history of cell divisions. Loss of heterozygosity (LOH) accumulates throughout the genome, offering large encoding capacity for phylogenetic inference of cell lineage.In this chapter, we demonstrate a method, using single-cell RNA sequencing, for reconstructing cell lineages from inferred LOH events in a Bayesian manner, annotating the lineage with cell phenotypes, and marking developmental time points based on X-chromosome inactivation. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and was initially developed to investigate Emx1+ cortical projection neuron and glia lineages from C57Bl/6J (B6) and CAST/EiJ (CA) interstrain F1 mice, describing progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis.

Animals↗

PubMed1977

Evolutionary changes of alpha-crystallin and the phylogeny of mammalian orders.

The sequences of the A chains of the eye lens protein alpha-crystallin from seventeen mammalian species were compared. They showed a generally slow rate of evolution, but with marked variations in different lineages. Most substitutions have occurred in the C-terminal part of the chain, which probably forms part of the surface of the alpha-crystallin aggregate. The ancestral sequence method of Dayhoff revealed interesting indications about the phylogenetic relationships between the eleven mammalian orders that were represented by the investigated species. Most evident was the divergence of marsupial and placental orders. A notable resemblance between the hyrax and elephant sequences was observed, setting them apart from the ungulates, including whale. Primates, rodents, lagomorphs, insectivores and tupaiids seem to derive from a common stem group. These phylogenetic inferences are discussed in relation to current palaeontological and taxonomical opinions, and compared to evidence from other protein sequence data.

Amino Acid Sequence↗

PubMed2026

Spatiotemporal patterns of Rift Valley fever virus in Africa: a retrospective genomic epidemiology and phylodynamic modelling study.

BACKGROUND: Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen causing outbreaks in humans and ruminants across Africa and the Arabian Peninsula. Originally restricted to the Great Rift Valley, RVFV has expanded geographically, prompting its classification by WHO as a pathogen of pandemic potential. We investigated the evolutionary and spatial dynamics of RVFV across Africa. METHODS: We used genomic data generated at the International Livestock Research Institute Nairobi genomic laboratory (BioProject PRJNA1106221) and combined with publicly available datasets retrieved from the National Center for Biotechnology (NCBI) GenBank nucleotide database. In retrieving RVFV genome sequences from the NCBI GenBank, we applied the search terms "Rift Valley fever virus segment L AND 6404[SLEN]", "Rift Valley fever virus segment M AND 3885[SLEN]", and "Rift Valley fever virus segment S AND 1520:1690[SLEN]" for L (Large), M (Medium), and S (Small) segments, respectively. For sequences without additional spatiotemporal information, we searched PubMed to extract the associated sequence metadata. We performed molecular clock analysis, phylogenetic inference, phylodynamic modelling (continuous phylogeographic reconstruction), and landscape phylogeography on the three RVFV genome segments (L, M, and S). We aimed to assess evolutionary rates, dispersal patterns, and environmental drivers. Focus was placed on lineage C, the most widely distributed variant. FINDINGS: The global dataset used in this study consisted of large (n=236), medium (n=237), and small (n=247), which were further filtered to exclude potential reassortants and vaccine strains. Genome sequences retrieved from NCBI GenBank database comprised large (n=180), medium (n=184), and small (n=202). The genome sequences from retrospective human and livestock isolates comprised large (n=56), medium (n=53), and small (n=45) collected in Burundi (2018), Kenya (2007, 2018, 2019, 2021, and 2022), and Rwanda (2018 and 2022). Our dataset revealed that RVFV exhibited low overall genetic diversity. Lineage C, however, showed evidence of active evolution, with substitution rates ranging from 3·58 × 10-4 to 9·76 × 10-4 substitutions per site per year. This lineage probably originated in Zimbabwe in the mid-1970s and has since expanded across eastern and southern Africa. Phylogeographic reconstructions revealed rapid spread, with diffusion coefficients exceeding 50 000 km2 per year. INTERPRETATION: Lineage C appears capable of establishing endemic transmission in new regions, with ongoing diversification observed during interepidemic periods. These observations reinforce the value of continuous genomic surveillance, particularly during cryptic transmission phases when adaptive mutations might emerge. Although further evidence is needed, observed trends in climate variability and land-use change point to the potential benefit of targeted surveillance in settings that could be at increased risk, including urban centres and wetlands. FUNDING: This work was supported by the German Federal Ministry for Economic Cooperation and Development, the Rockefeller Foundation, and the Africa Centres for Disease Control and Prevention.

Rift Valley fever virus↗

PubMed2026

Comparison of paralog identification methods and their impact on species tree topologies in target capture phylogenomics within the Sindora clade (Detarioideae: Leguminosae).

Target capture is a common method of generating high throughput DNA sequencing data for phylogenetic reconstruction of species relationships, for which single copy genes are usually most informative. However, a pervasive problem with target capture is that putatively single copy genes may in fact be paralogs resulting from gene duplication, which are problematic for phylogenetic inference because their evolutionary history may differ from the divergence history of species. Here, we use as a case study a target enrichment dataset of 88 species of Detarioideae (Leguminosae) with a focus on the Sindora clade to examine approaches for handling paralogs, including the built-in paralog handling functions in HybPiper and CAPTUS, plus subsequent steps using Putative Paralog Detection and the tree-based Yang & Smith orthology inference approach. We compare the paralogs flagged using these methods and verify their performance with BLAST mapping against a reference genome sequence of Sindora glabra, and then subsequently compare the species tree topologies produced across these methods. Our comparisons of paralogs flagged across the Sindora clade show that the Putative Paralog Detection pipeline was the most accurate in identifying paralogs in terms of its similarity to the BLAST mapping, followed by the built-in paralog identification function of CAPTUS. However, the results we recovered for the Detarioideae subfamily suggest that the largest differences in species tree topology resulted from the use of paralog-filtered alignments (such as with the Putative Paralog Detection pipeline and the Yang & Smith orthology inference approaches) rather than just by removing the sequences of identified paralogous genes. This was the true for HybPiper-assembled datasets but was not seen in CAPTUS-assembled datasets. In all comparisons, the topological differences caused by different paralog handling methods tended to be confined to clades where processes such as hybridisation and introgression are prevalent. Our study provides a roadmap to establish the best approach to identify, eliminate or separate paralogs in the absence of a chromosomally contiguous reference genome for a study group, and highlights the importance of careful data inspection and processing in addition to understanding the extent of paralogy and paralog characteristics (e.g. sequence divergence between copies) for their study group.

Phylogeny↗