Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution from common ancestors. However, they often lack the flexibility to represent processes like introgressive hybridization, which leads to gene flow between taxa. Phylogenetic networks generalize trees but typically assume that ancestral taxa merge instantaneously to form "hybrid" descendants. In contrast, convergence-divergence models retain a single underlying "principal tree" and permit gene flow over arbitrary time frames. They can also model other biological processes leading to taxa becoming more similar, such as replicated evolution. We present novel maximum likelihood algorithms to infer most aspects of N-taxon convergence-divergence models - many consistently - using a quartet-based approach. All algorithms use 4-taxon convergence-divergence models, inferred from subsets of the N taxa using a model selection criterion. The first algorithm infers an N-taxon principal tree; the second infers sets of converging taxa; and the third infers model parameters - root probabilities, edge lengths and convergence parameters. The algorithms can be applied to multiple sequence alignments restricted to genes or genomic windows or to gene presence/absence datasets. We demonstrate that convergence-divergence models can be accurately recovered from simulated data.

The 'silent pandemic' of antimicrobial resistance (AMR) represents a significant global public health threat. AMR genes in bacteria are often carried on mobile elements, such as plasmids. The horizontal movement of plasmids allows AMR genes and resistance to key therapeutics to disseminate in a population. However, the quantification of the movement of plasmids remains challenging with existing computational approaches. Here, we introduce a novel method that allows us to reconstruct and quantify the movement of plasmids in bacterial populations over time. To do so, we model chromosomal and plasmid DNA co-evolution using a joint coalescent and plasmid transfer process in a Bayesian phylogenetic network approach. This approach reconstructs differences in the evolutionary history of plasmids and chromosomes to reconstruct instances where plasmids likely move between bacterial lineages while accounting for parameter uncertainty. We apply this new approach to a five-year dataset of Shigella, exploring the plasmid transfer rates of five different plasmids with different AMR and virulence profiles. In doing so, we reconstruct the co-evolution of the large Shigella virulence plasmid with the chromosome DNA. We quantify higher plasmid transfer rates of three small plasmids that move between lineages of Shigella sonnei. Finally, we determine the recent dissemination of a multidrug-resistant plasmid between S. sonnei and S. flexneri lineages in multiple independent events and through steady growth in prevalence since 2010. This approach has a strong potential to improve our understanding of the evolutionary dynamics of AMR-carrying plasmids as they are introduced, circulate, and are maintained in bacterial populations.

The golden hind grouper (Cephalopholis aurantia) is a visually striking reef fish of high economic value in the Coral Triangle region, serving both as a food source and as an ornamental species in the aquarium trade. In addition to its economic significance, C. aurantia plays an important ecological role in maintaining the balance of coral reef ecosystems. However, the species is facing serious threats due to increasing fishing pressure and exploitation, often carried out without strict regulatory oversight. Assessing genetic variation is thus essential for understanding population diversity and structure, enabling the development of effective conservation strategies, particularly under intensifying environmental and anthropogenic stress. In this study, we examined the genetic diversity and population structure of C. aurantia in the Spratly Islands using the mitochondrial Cytochrome c Oxidase subunit I (COI) gene. This gene is a widely recognized marker in population genetics of marine fish. A total of 30 individuals were successfully sequenced, and COI variability was assessed. Results revealed high haplotype diversity but low nucleotide diversity, indicating a genetic disequilibrium within the population. Neutrality tests and population dynamic analyses supported a scenario of post-bottleneck demographic expansion. Phylogenetic and haplotype network analyses further corroborated this hypothesis, showing a dominant haplotype with closely related satellite haplotypes, along with evidence of new haplotypes entering the population. Such patterns may be driven by larval dispersal capabilities, strong reproductive potential, and the influence of oceanic currents facilitating gene flow. Documenting signs of population expansion and immigration is crucial for spatially explicit management and conservation of C. aurantia, ensuring the long-term sustainability of this ecologically and economically significant species in the Spratly Islands.

"Normal" phylogenetic networks may be emerging as the leading class.

Mitochondrial genome analysis supports zoonotic transmission of triclabendazole-resistant human fascioliasis in Peru

Phylogenetic and Biochemical Analysis of the Evolution and Interdomain Modularity of Bifunctional L-Fucokinase/GDP-Fucose Pyrophosphorylases.

Phylogenomic insights into incomplete lineage sorting and hybridization in early-diverging eudicots.

Haemosporidians (Haemosporida, Apicomplexa), which include malaria parasites, are found in nearly all terrestrial ecosystems. Avian haemosporidians have been extensively studied; however, there is limited information on parasites in owls (order Strigiformes). Here, haemosporidians infecting North American owls were characterized using an integrative methodology. Taking advantage of injured/dead owls from rehabilitation centres in the central and northeastern USA, 53 individuals of Bubo virginianus, Strix varia, Megascops asio, Bubo scandiacus, Aegolius acadicus, and Tyto furcata were screened using polymerase chain reaction for all samples and microscopy for those with available blood smears. Parasite mitochondrial genomes were obtained using a long-read sequencing method (PacBio HiFi), which efficiently detects multiple infections in a single host. The relationships between parasite lineages were estimated using phylogenetic and haplotype network methods. In total, 21 individuals from three species were positive by PCR: B. virginianus (14/17, 82.4%), M. asio (3/5, 60%), and S. varia (4/8, 50%). Two Plasmodium, three Haemoproteus, and four Leucocytozoon lineages were identified infecting these hosts, with one Haemoproteus and one Leucocytozoon being new to science. All positive individuals were infected with Haemoproteus parasites, and two B. virginianus had a mixed infection with Leucocytozoon and Haemoproteus species. The hSTVAR01 cytochrome b (cytb) lineage common in North America is linked for the first time to Haemoproteus syrnii. Haemoproteus syrnii was found in all 14 positive B. virginianus and two S. varia. Notably, all the cytb lineages from previously identified H. syrnii, based on erythrocytic stages, were not monophyletic, indicating the existence of an undescribed species. The pPADOM11 cytb lineage was recognized as an allele of Plasmodium elongatum. Long reads enabled the detection of mixed/co-infections. The link between genetic data and morphospecies was established in two cases. Several Leucocytozoon clades were observed; however, only one morphospecies, Leucocytozoo danilewskyi, has been described in owls. Thus, there is a need for a detailed analysis of blood stages to determine whether different owl Haemoproteus and Leucocytozoon parasites exhibit morphological differences or represent cryptic species. Overall, this study underscores the importance of high-quality molecular data in characterizing the biodiversity of haemosporidian parasites.

A core goal of phylogenomics is to determine the evolutionary history of a set of species from biological sequence data. Phylogenetic networks are able to describe more complex evolutionary phenomena than phylogenetic trees but are more difficult to accurately reconstruct. Recently, there has been growing interest in developing methods to infer semi-directed phylogenetic networks. As computing such networks can be computationally intensive, one approach to building such networks is to puzzle together smaller networks. Thus, it is essential to have robust methods for inferring semi-directed phylogenetic networks on small numbers of taxa. In this paper, we investigate an algebraic method for performing phylogenetic network inference from nucleotide sequence data on 4-leaf semi-directed phylogenetic networks by analysing the distribution of leaf-pattern probabilities. On simulated data, we found that we can correctly identify with high accuracy the undirected phylogenetic network for sequences of length at least 10kbp. We found that identifying the semi-directed network is more challenging and requires sequences of length approaching 10Mbp. We are also able to use our approach to identify tree-like evolution and determine the underlying tree. Finally, we employ our method on a real dataset from Xiphophorus species and use the results to build a phylogenetic network.

Objective: This study conducted a comprehensive analysis of molecular transmission networks and pretreatment drug resistance (PDR) in newly diagnosed HIV-1 infections in Taizhou, China. Methods: From 2021 to 2023, we collected 1126 plasma samples from newly diagnosed HIV patients in Taizhou. The HIV pol gene was amplified, and the obtained sequence was used to construct a maximum likelihood (ML) phylogenetic tree and molecular transmission network. PDR-related mutations were analyzed based on the Stanford University HIV Resistance Database. We conducted genotyping analysis and analysis of factors related to the larger clusters (≥10). Results: We successfully amplified and sequenced the pol region from 937 (83.2%, 937/1126) treatment-naïve HIV-1 patients, each with comprehensive epidemiological documentation. Phylogenetic characterization revealed significant subtype heterogeneity, with CRF07_BC (42.1%, 395/937), CRF01_AE (27.6%, 259/937) and CRF08_BC (22.1%, 209/937) being the most prevalent. Notably, 11.4% of the sequenced population (107/937) presented detectable PDR mutations. Univariate analysis revealed that larger clusters (≥10) are more inclined to be aged ≥60, divorced or widowed, have high or technical secondary school education, and have sexual contact with homosexuality. Multivariate analysis revealed that age ≥60 years and not having a PDR mutation (p < 0.05) were factors associated with larger clusters (≥10). Conclusions: Molecular transmission networks suggest that CRF08_BC is spreading rapidly among the older male population. Consequently, targeted interventions aimed at this population are crucial for halting the ongoing rapid dissemination of this subtype.

ABSTRACTIslands provide unique opportunities to study historical biogeography, acting as both cradles of endemism and active corridors for species dispersal. The Sicilian Channel, which separates Sicily from the Maghreb, exemplifies this complexity. We investigated the colonisation history of the lesser horseshoe bat (Rhinolophus hipposideros) on Pantelleria Island (southern Italy) to assess whether its population derives from Europe or North Africa. Because R. hipposideros has limited dispersal ability and is largely sedentary, its occurrence on Pantelleria raises questions about past connectivity across the Channel. We analysed mitochondrial markers (COI, cyt‐b, 12S) from Pantelleria, Malta, Algeria, and across the species' range. Phylogenetic and haplotype network analyses place Pantelleria and Malta in a well‐supported clade sister to North African lineages and distinct from European populations. Time‐calibrated analyses based on cyt‐b suggest that the Pantelleria–Malta group diverged from North African conspecifics around 200,000 years ago (MIS 7.2). A palaeogeographical reconstruction for this interval indicates lowered sea level reduced the marine gap between Pantelleria and Tunisia to about 68 km, consistent with over‐sea colonisation from North Africa. The short available sequences for conspecific European bats suggest considering these inferences as provisional. Within these limitations, our results are most consistent with a Maghrebian origin for Pantelleria's R. hipposideros, while alternative routes (including European sources) cannot be excluded. Broader genomic sampling, especially from Sicily and Morocco, will be required to resolve colonisation direction and fully establish the population's biogeographic history. More generally, our findings reinforce the view of the Sicilian Channel as an asymmetrically permeable biogeographic corridor that can facilitate faunal exchange across the central Mediterranean.

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying gene or species trees. This results in orthology graphs, where each vertex represents a gene, and an edge exists between two vertices if the corresponding genes are estimated to be orthologs. Orthology graphs inferred under a tree-like evolutionary model must be cographs. However, real-world data often deviate from this property, either due to noise in the data, errors in inference methods or, simply, because evolution follows a network-like rather than a tree-like process. The latter, in particular, raises the question of whether and how orthology graphs can be derived from or, equivalently, are explained by phylogenetic networks. In this work, we study the constraints imposed on orthology graphs when the underlying evolutionary history follows a phylogenetic network instead of a tree. We show that any orthology graph can be represented by a sufficiently complex level-k network. However, such networks lack biologically meaningful constraints. In contrast, level-1 networks provide a simpler explanation, and we establish characterizations for level-1 explainable orthology graphs, i.e., those derived from level-1 evolutionary histories. To this end, we employ modular decomposition, a classical technique for studying graph structures. Specifically, an arbitrary graph is level-1 explainable if and only if each primitive subgraph is a near-cograph (a graph in which the removal of a single vertex results in a cograph). Additionally, we present a linear-time algorithm to recognize level-1 explainable orthology graphs and to construct a level-1 network that explains them, if such a network exists. Finally, we demonstrate the close relationship of level-1 explainable orthology graphs to the substitution operation, weakly chordal and perfect graphs, as well as graphs with twin-width at most 2.

In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations connect the space of all phylogenetic networks on the same set of leaves, even if we forbid contractions that create cycles. This allows to define an operational distance on this space, as the minimum number of contractions and expansions required to transform one network into another. We highlight the difference between this distance and the computation of the maximum common contraction between two networks. Given its ability to outline a common structure between them, which can provide valuable biological insights, we study the algorithmic aspects of the latter. We first prove that computing a maximum common contraction between two networks is NP-hard, even when the maximum degree, the size of the common contraction, or the number of leaves is bounded. We also provide lower bounds to the problem based on the Exponential-Time Hypothesis. Nonetheless, we do provide a polynomial-time algorithm for weakly galled trees, a generalization of galled trees.

We aimed to elucidate the spatiotemporal origins and biogeographic history of Polynesian blueberries within Vaccinium sect. Myrtillus, specifically those endemic to Hawai'i and the closely related V. cereum in southeastern Polynesia. A HybSeq data set was constructed for Polynesian Vaccinium and added to a previously published data set for tribe Vaccinieae. Phylogenomic, ancestral area, fossil-calibrated divergence time, and phylogenetic network analyses were conducted to assess the origin and biogeographic history of the group. Hawai'ian taxa plus a sample of Vaccinium cereum from Ua Pou Island formed a clade that was phylogenetically nested within continental Vaccinium sect. Myrtillus. The clade was inferred to have originated from temperate East Asia ca. 7.1-5.2 million years ago, dispersing to Kaua'i either directly or via one of the subsident or now-submerged Northwestern Islands of the archipelago. Nuclear-plastid genome discordance and network analysis corroborated the previously hypothesized hybrid origin of V. cereum and suggested a possible dispersal from Hawai'i to coastal North America followed by introgression into the mainland species V. ovalifolium. Our study suggests that an ancestral exaptation to temperate climates and an evolutionary history of the Hawai'ian Vaccinium clade dating back at least to the origin of Kaua'i have likely contributed to the present-day diversity of the group. Our results support a temperate East Asian origin, rare among the native plants of Hawai'i, and highlight the ongoing potential for both short- and long-distance dispersal in this group of island plants without a reduction or loss of dispersibility.

Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.

Molecular epidemiology and cross-species transmission risk of Enterocytozoon bieneusi between humans and livestock: Evidence from Lishui, China

Filarioid nematodes are harmful vector-borne pathogens that afflict humans and other animals, with numerous species transmissible from animals to humans, i.e., zoonotic. In the last decade, one zoonotic filarioid, previously named Dirofilaria sp. Hong Kong genotype has been increasingly found as a cause of disease in people traveling from South Asia and has recently been characterized as a novel species: Dirofilaria asiatica. Nonetheless, the epidemiology of this parasite in Asia remains poorly understood. Therefore, with the aid of a novel pan-filarioid nanopore-based metabarcoding assay, we aimed to elucidate the epidemiology of dirofilariosis in Cambodia. We tested 504 canine blood samples collected from five regions and used the cytochrome c oxidase (cox1) gene sequences obtained to conduct phylogenetic analyzes. We found no evidence of the canine heartworm Dirofilaria immitis nor Dirofilaria repens in the country. Conversely, we detected D. asiatica and genetically characterized it from the eastern district of Tbong Khmum at a local prevalence of 4% (95% CI = 1.6%-9.8%), an area just ~100 km northeast of the country's capital, Phnom Penh. We also detected Acanthocheilonema reconditum from 0.2% of dogs sampled (95% CI = 0%-1%). Phylogenetic and haplotype network analyzes of Cambodian D. asiatica sequences clustered with strong support to those found from canines and humans in Bhutan, Hong Kong, India, and Sri Lanka. This genetic characterization of D. asiatica in Cambodia highlights the need for further epidemiological research into human filariases in Cambodia, given the zoonotic nature of this parasite and that mass drug administration targeting filarioids is no longer conducted in the country.IMPORTANCEParasitic filarioid nematodes are transmitted by blood-sucking arthropods and can cause significant disease in animals and humans (i.e., zoonotic). One such zoonotic filarioid (Dirofilaria asiatica) that has recently been characterized has been found responsible for a growing number of cases of human filariases, particularly in individuals who live in or have traveled to South and Southeast Asia. D. asiatica predominantly infects dogs, and therefore, to better understand this parasite's distribution, we tested 504 dogs from five regions of Cambodia using an advanced diagnostic approach. We found that the local prevalence of D. asiatica in dogs in the eastern district of Tbong Khmum was 4%. Given that mass drug administration programs to control human-infecting filarioid nematodes in Cambodia have stopped, this first detection of D. asiatica in Cambodia is alarming, given its potential to cause disease in vulnerable cohabiting people.

Understanding the evolutionary and geographic trajectories of crop wild relatives is vital for enhancing agro-biodiversity and advancing climate-resilient agriculture. This study focuses on ten Vicia L. taxa—comprising five species, four varieties, and one subspecies—of significant agricultural importance in Türkiye. An integrative molecular framework was applied, incorporating nuclear ITS sequence data, ITS2 secondary structure modeling, phylogenetic network analysis, and time-calibrated biogeographic reconstruction. This approach revealed well-supported clades, conserved secondary structural elements, and signatures of reticulate evolution, particularly within the Vicia sativa L. and V. villosa Roth. complexes, where high genetic similarity suggests recent divergence and possible hybridization. Anatolia was identified as both a center of origin and a dispersal corridor, with divergence events estimated to have occurred during the Late Miocene–Pliocene epochs. Inferred migration routes extended toward the Balkans, the Caucasus, and Central Asia, corresponding to paleoenvironmental events such as the uplift of the Anatolian Plateau and the Messinian Salinity Crisis. Phylogeographic patterns indicated genetic affiliations between Turkish taxa and drought-adapted Irano-Turanian lineages, offering valuable potential for climate-resilient breeding strategies. The results establish a molecularly informed foundation for conservation and varietal development, supporting sustainability-oriented innovation in forage crop systems and contributing to regional food security.

Bounding the number of reticulation events for displaying multiple trees in a phylogenetic network

The yellowfin seabream (Acanthopagruslatus), a commercially important marine fish in Vietnam, faces threats from overfishing and habitat degradation and requires a deeper understanding of its genetic structure and evolutionary history for effective conservation. This study investigated the genetic diversity, population structure and demographic history of A.latus across three populations in Central Vietnam using mitochondrial control region (mtCR) sequences and multivariate analyses. A total of 125 fish samples were collected between January 2023 and June 2024, with DNA extracted from pectoral fin tissues and amplified for mtCR sequencing. Phylogenetic and haplotype network analyses revealed three main haplogroups with high genetic diversity (haplotype diversity: 0.993 ± 0.002), but minimal population differentiation (Fst = 0.00029, p = 0.39188), indicating significant gene flow, facilitated by coastal currents as these populations maintain strong genetic connectivity with the coastal populations of southern China. Neutrality tests, mismatch distribution and Bayesian Skyline Plots have suggested a historical population expansion followed by recent stability and slight decline. These findings highlight the species’ resilience, but underscore the need for regionally coordinated conservation strategies to protect critical habitats like estuaries and mangroves, ensuring the sustainability of A.latus populations in Vietnam.