Understanding macroevolution requires integrating morphological and molecular data from fossil and extant taxa to reconstruct phylogenies, trait evolution and biogeographic history. However, the macroevolutionary process since its deep-time origin via a total-evidence approach has been investigated only in a limited number of groups. Here we present the first total-evidence phylogenetic and biogeographic analyses of Dilaridae, a key transitional group of Neuroptera, integrating high-resolution 3D morphological reconstructions of Cretaceous stem-group taxa. We describe a new genus and four new species from the Kachin amber, that is, †Palaeonallachius fangyuani gen. et sp. nov., †Coronidilar jiaxiaoae sp. nov., †Cretodilar zhiqiae sp. nov. and †Cretodilar galaxias sp. nov., which provide valuable morphological data for phylogenetic inference. Comparative analyses using alternative sampling strategies (extant-only or total-evidence) demonstrate the advantages of integrating fossil data in phylogenetic inference, divergence-time estimation and ancestral range reconstruction. Our results support a Gondwanan origin of Dilaridae associated with the West Burma Block, followed by dispersal into Laurasia via northward-drifting Gondwanan landmasses and possible trans-Antarctic dispersal since the Jurassic. The absence of extant dilarids in Australasia is likely due to extinction. These findings highlight the importance of fossil integration in resolving deep-time evolution and the role of Gondwanan dynamics in shaping insect biogeography.
The Chinese caterpillar fungus Ophiocordyceps sinensis has colonized the extreme high-elevation environment of the Qinghai-Tibet Plateau despite severe cold, hypoxia and intense UV radiation. We analysed 305 whole genomes, including 69 newly sequenced genomes, and resolved nine phylogenetic clades with a mosaic geographic distribution, with the Hengduan Mountains acting as both a diversity centre and a corridor for gene flow. These clades represent three evolutionary regimes: early lineages (Clades 1-4) primarily shaped by incomplete lineage sorting (ILS), intermediate lineages (Clades 5-8) shaped by the combined effects of ILS and introgression, and the most recent lineage (Clade 9) associated with candidate signatures of selection. Functional analyses revealed that ILS retained pathogenicity-related genes, introgression introduced adaptations in RNA processing, mitochondrial transport and lipid metabolism and candidate regions under selection targeted UV-damage repair and DNA replication. Together, these results demonstrate how ILS, introgression and selection-associated genomic changes acted sequentially to maintain parasitic lifestyle, enable environmental adaptation and drive rapid radiation under extreme alpine conditions.
In well-studied groups of organisms, the taxonomic landscape can be very complex, with several alternative classifications describing diversity within the same set of populations. For example, three hypotheses have previously been proposed to describe the taxonomy of the common and widespread Eurasian Dusky Meadow Brown butterfly, Hyponephele lycaon, and its close relatives. The morphology-based hypothesis (1) is explicitly based on genital differences between two putative species. The other two hypotheses, the hypothesis of multiple allopatric species (2) and the hypothesis of two sympatric species (3) within the H. lycaon complex, are based on scientific intuition rather than on rigorous data and analyses. Here, using an integrative taxonomic approach, we cannot confirm any of the previous classifications, although elements of each can be found in the suggested new system. As a result, we show that Dusky Meadow Brown butterfly is a triplet of sibling species. Two of them, H. collina (Turkey, Levant, Iran) and H. lycaon (Europe, temperate Asia), are allopatric. The third species, H. libanotica, is widely sympatric with H. collina in Turkey, Israel and Iran. We argue that past taxonomic hypotheses, including those based on implicit evidence, are useful priors for planning sampling strategies and more detailed modern taxonomic analyses.
Oropouche virus (OROV) is a high-risk emerging arbovirus that causes recurrent febrile outbreaks across tropical Central and South America, posing persistent public health threats with expanding endemic ranges and rising zoonotic spillover risks. Limited comprehensive evidence regarding its genomic plasticity and multi-scale evolutionary dynamics hinders precise epidemic prevention. Herein, we performed systematic phylogenomic analyses of all available OROV sequences to elucidate its recombination profiles, adaptive evolution, cross-species transmission and spatial dispersal patterns. Phylogenetic reconstruction based on breakpoint-free regions revealed two major polyphyletic lineages characterized by extensive multi-host and transboundary circulation, with Brazilian strains dominating global OROV populations. Bayesian ancestral inference identified humans as the likely earliest detectable ancestral host, while all statistically robust host-switching events were closely associated with Callithrix spp., confirming their critical role as intermediate amplifying hosts. Phylogeographic analyses suggested Brazil and Peru as the primary ancestral origins, with neighbouring short-distance diffusion and frequent cross-border transmission forming a multi-path dissemination system concentrated in the Amazon Basin and southeastern coastal zone of Brazil. Pronounced topological incongruence among L, M and N genes demonstrated pervasive segmental reassortment, which has intensified temporally since 2010, especially during 2020-2024. Notably, the M gene undergoes intensive intra-segment recombination and prominent positive selection with relaxed functional constraints, representing the key adaptive hotspot, whereas L and N genes remain highly conserved under strong purifying selection. This study clarifies the synergistic evolutionary mechanisms of recombination, reassortment, host switching and differential selection, providing robust theoretical support for OROV surveillance and targeted intervention.
A new family, †Eotenthredinidae, including two new species, †Eotenthredo sinensis gen. et sp. nov. and †Eotenthredo magna sp. nov., is described, based on nine adult specimens from the Early Cretaceous Yixian Formation, ~125 Ma. As the oldest known crown tenthredinoids to date, †Eotenthredinidae exhibits a mosaic of plesiomorphic and derived traits, serving as a crucial transitional taxon linking stem and crown tenthredinoids. We conduct a morphology-based phylogenetic analysis of Tenthredinoidea incorporating the most extensive sampling of Mesozoic fossils to date. Our results support the monophyly of Tenthredinoidea, recover the †'Xyelotomidae' as a paraphyletic grade and place †Eotenthredinidae as the sister group to core tenthredinoids. Morphometric analyses of the mesothorax further support the intermediate position of †Eotenthredinidae. Combining lineage-through-time analyses of plants and statistical analysis of tenthredinoid fossils, we emphasize the deep-time evolutionary association between tenthredinoids and their host plants. This study provides critical paleontological evidence for clarifying the early evolutionary history of Tenthredinoidea and deepens our understanding of plant-insect co-evolution and ecosystem restructuring during the Cretaceous Terrestrial Revolution from the insect perspective.
A long-standing challenge in phylogenomics has been the resolution of relationships originated from ancient radiations. In these cases, phenomena such as incomplete lineage sorting can increase the support for conflicting resolutions. Most of the diversity in the Class Bivalvia originated during an Ordovician radiation; indeed, several deep relationships among Bivalvia have not been fully resolved yet. Traditionally, Heterodonta clusters the Subclasses Archiheterodonta and Euheterodonta; however, recent analyses supported Archiheterodonta as sister to the other Subclass Palaeoheterodonta (A + P). Until now, Archiheterodonta was the last major Bivalvia clade lacking a genome assembly: we sequenced the genome of Cardita leana (Archiheterodonta, Carditidae) and inferred the phylogeny from a supermatrix including 64 bivalve species. Although different methods supported Heterodonta, many genes (27% of the dataset) favoured Archiheterodonta + Palaeoheterodonta (A + P). This discordance could not be ascribed to any systematic phylogenetic biases. However, divergence times obtained from the respective supporting genes datasets placed the origin of Heterodonta significantly deeper than the origin of A + P, appearing inconsistent with the fossil record. This suggests that genes supporting Heterodonta reflect ancestral polymorphisms that persisted in Archiheterodonta and Heterodonta lineages through incomplete lineage sorting. Overall, we suggested a phylogenomic framework to study deep radiations and showed that A + P represents a plausible hypothesis.
Homalonotidae is a morphologically distinctive trilobite family well known in systematics studies, yet phylogenetic studies remain scarce. This study investigated internal relationships among taxa within the Homalonotidae family and reassessed the classification of problematic species. A phylogenetic analysis was conducted using a matrix composed of 36 taxa and 56 morphological characters of the trilobite exoskeleton. Analysis under the TBR algorithm recovered eight most parsimonious trees, from which a strict consensus tree was obtained. The results revealed substantial inconsistencies in the diagnosis of several genera and species, particularly due to the presence of paraphyletic and polyphyletic groupings. Some taxa, such as Burmeisteria fontinalis, Dipleura dekayi, and Burmeisterella braziliensis, remained phylogenetically stable and well-supported. Conversely, certain species traditionally assigned to Burmeisteria, including B. oiara and B. antarcticus, behaved as wild-cards within the trees, leading to their reclassification as Burmeisteria sp. Moreover, strong phylogenetic correlations were identified between species from different genera. These findings challenge the current taxonomic framework and allow for the proposal of new taxonomic arrangements. Furthermore, the relationships among the taxa indicate that Devonian Homalonotidae reflect a complex palaeobiogeographic system and further suggests that the Gondwana basins functioned as a dynamically connected network during the Devonian period.
During the COVID-19 pandemic, the need for quick public health action often conflicted with the careful methods required in phylogenetics. To explore this, we reviewed 217 SARS-CoV-2 studies published from January 2020 to March 2025 in 121 journals. We found many methodological problems that weaken the reliability and reproducibility of these studies. Key issues include missing outgroup sampling, which affects ingroup topology, tree rooting and how we interpret evolutionary changes and relationships. Another issue is the lack of gene annotations, which can cause characters from one gene to align with those of a different gene. Many studies also misinterpret support or other branch statistics, treating them as proof of clade accuracy instead of as measures of relative evidence. In addition, 91% of the studies do not follow FAIR (Findable, Accessible, Interoperable, and Reusable) data principles, with data and code often unavailable. Finally, we also found a "prestige paradox": journals with higher impact factors do not necessarily have better methods or transparency. Therefore, we offer simple guidelines for authors, reviewers and editors to improve transparency and FAIR data standards in viral phylogenetics, making writing and reviewing papers easier, ensuring published phylogenetic analyses remain a trustworthy resource for future pandemics.
Cingulata, a major lineage of Xenarthra, comprises extinct and extant armoured placental mammals that diversified throughout the Cenozoic. Despite extensive study, phylogenetic hypotheses based on morphological and molecular data remain incongruent, and no total evidence analysis has been conducted. Here, we integrate the largest morphological dataset for cingulates with molecular and stratigraphic data to infer their phylogeny, divergence times, and diversification dynamics. Morphological data were analysed under maximum parsimony (MP), assessing sensitivity to alternative settings, and under Bayesian inference (BI), exploring state-space partitioning and model adequacy. Combined analyses were conducted under MP, maximum likelihood, and tip-dating BI under a skyline fossilized birth-death model. Results support the monophyly of Cingulata and recover two main clades, Paracingulata and Eucingulata. Eucingulata includes Dasypodoidea and Chlamyphoroidea, the latter comprising Euphracta and Glyptodonta. Divergence estimates indicate Paleogene origins for family-level clades, with most intra-familial diversification predating the Neogene. Diversification analyses reveal increased origination during the Miocene, followed by reduced origination in the Pliocene and elevated extinction in the Quaternary. This study presents the most comprehensive phylogenetic framework for cingulates, clarifying long-standing conflicts between morphological and molecular evidence, and updating their classification, with higher level groups redefined to reflect phylogenetic structure, morphological distinctiveness, and divergence times.
Pinworms (Nematoda: Oxyurida) are among the first documented zooparasitic nematodes, and some species are of veterinary, medical, and economic importance. However, the basic molecular phylogenetic framework for the Oxyurida is far from comprehensive, and the origin and early evolutionary history of the group remain little understood. In this study, phylogenomic analyses of the Oxyurida, involving the most comprehensive family-level taxon sampling of pinworms to date, were performed based on the universal single-copy orthologues and the mitochondrial protein-coding genes. Phylogenomic results yielded a highly resolved tree that confirmed the validity of the family Gyrinicolidae, suggested that the Heteroxynematidae is nested within the Oxyuridae and should be treated as a subfamily within the latter family (Heteroxynematinae status novus), and failed to support the separation of the subfamilies Oxyurinae and Syphaciinae. Using fossil-based time priors to calibrate both mitogenomic and genomic phylogenies, we establish the first comprehensive evolutionary timescale for pinworms. Our results place the most recent common ancestor of the Oxyurida in the late Devonian and further support the hypothesis that members of the vertebrate-parasitic Oxyuroidea initially parasitized reptiles and later extended their host range to mammals, and during this transition, opportunistically produced a highly specialized lineage infecting anuran tadpoles.
Replicated pairs of ancestral and evolutionarily derived populations provide opportunities to test hypotheses about the deterministic laws of evolution. The Asellus aquaticus species complex is an invertebrate model system with several independent surface-to-cave transitions and a complicated and unresolved evolutionary history. Here, we sampled all known major lineages and surface-cave population pairs, and used genome-wide ddRAD sequencing to improve phylogenetic resolution. We present a robust phylogenetic backbone that is essential for testing hypotheses of ecological transitions, trait evolution and comparative analyses. Our results support an emerging new perspective on the evolution of cave invertebrates from surface ancestors. First, frequent admixture between distinct surface lineages may preclude pinpointing a single surface sister lineage for each cave colonization. Second, the mitochondrial genomes of some cave lineages have been replaced by mitogenomes of adjacent surface populations during sporadic Pleistocene hybridization events. The resulting new phylogenetic view of Asellus aquaticus is one of continuously admixing surface lineages with several isolated cave lineages budding off from the omnipresent surface progenitor. Some cave lineages have been described as separate species. Hence, the taxonomic structure of the species complex is shaped by ecologically driven budding speciation rather than by a usual succession of dichotomous lineage splits.
This paper discusses cases where the "majority rule supertree (-)" method of Cotton and Wilkinson (Syst. Biol. 2007, 56, 445) prefers the relationships displayed by a minority of the trees, and is contradicted by the majority. When the trees have different numbers of taxa, the relationships of the bigger tree can be more influential (depending on the specific arrangement of the taxa found in the larger tree but not in the smaller ones). In that case, the smaller tree can occur in an arbitrarily large number of identical copies, and still be disregarded if the big tree has a sufficiently large number of taxa. The "majority rule supertree (+)" method, by contrast, collapses the groups in the bigger tree (instead of resolving them in favour of the bigger tree, as the (-) version).
We investigated the phylogeny and historical biogeography of the cosmopolitan velvet ant tribe Trogaspidiini (Hymenoptera: Mutillidae: Mutillinae) using ultraconserved element (UCE) data. Thirty-six of forty-five described trogaspidiine genera and subgenera were represented by 95 ingroup species, and the monophyly of the New World genus Timulla Ashmead, 1899 was tested using 40 species. Maximum parsimony and maximum likelihood analyses were conducted on an aligned dataset of 1 148 582 characters. Trogaspidiini was recovered as polyphyletic, with Dolichomutilla Ashmead, 1899 placed in Mutillini. Timulla was recovered as monophyletic and sister to a clade of Ethiopian and Oriental trogaspidiines. The Trogaspidia complex and Trogaspidia Ashmead, 1899 (sensu Nonveiller) were recovered as polyphyletic. The five non-nominate subgenera of Trogaspidia are therefore elevated to genus rank: Acutitropidia Nonveiller, 1995, Arcuatotropidia Nonveiller, 1995, Chilotropidia Nonveiller, 1995, Inflatispidia Nonveiller, 1995, and Lobotropidia Nonveiller, 1995, all new status. Oriental species currently placed in Trogaspidia are considered misclassified. Ancestral area analyses suggest an early diversification of Trogaspidiini in the Ethiopian region with repeated exchange between Ethiopian and Oriental regions. Timulla is estimated to have an Ethiopian or Oriental ancestor, with Neotropical North America as the possible ancestral range within the New World.
Monotypic genera are undesirable from a cladistic perspective because they are not clades and therefore cannot be diagnosed by synapomorphies. They are undesirable from a nomenclatural perspective because their names obscure the relationship of the contained species to other species, thereby negating the semantic value of the generic name. This essay reviews situations in which monotypic genera are required by the structure of a cladogram, and situations in which they have apparently been erected on phenetic or evolutionary taxonomic considerations. A case study from Hesperiidae (skipper butterflies) is presented.
We present a morphology-based backbone phylogeny of Cerambycidae beetles inferred by parsimony analyses using 77 adult characters scored for 101 species. This phylogeny is largely consistent with recent phylogenomic studies regarding key placements (e.g., Parandrini stat. rev. within Prioninae, Necydalini stat. rev. within Lepturinae, the sister-group relationship of Cerambycinae with Prioninae (including Parandrini), the monophyly of Saperdini, the non-monophyly of some Lamiinae tribes), while differing primarily in the position of Lamiinae. By testing various character and taxon-sampling partitions we revealed that some of the most variable external characters and all genital characters (without exploring aedeagal internal sac) have low phylogenetic signal, but still the more inclusive analyses are the most robust. Across all our analyses, Cerambycidae s.l. are consistently recovered as monophyletic, with Disteniinae stat. rev., Vesperinae stat. rev., and Oxypeltinae stat. rev. placed inside or adjacent to the core Cerambycidae s.s. clade depending on character sampling. Our results highlight the strength of phylogenomics in providing a robust framework for higher-level relationships, but also emphasize that morphology-based analyses remain indispensable for identifying and interpreting the character systems that define those relationships. This study exemplifies complementarity of morphological and genomic evidence, while providing a broad morphology-based phylogenetic analysis of Cerambycidae.
The family Turdidae (Aves, Passeriformes) is a diverse clade of passerine birds that presents a global distribution across a wide range of environments. While numerous studies have addressed the biogeography of specific genera, the family's origins remain largely unresolved. To reconstruct this taxon's biogeographic history, we compiled genetic and geographic range data from public sources. This information was used to build a time-calibrated phylogeny based on a concatenated dataset of mitochondrial and nuclear genes for 155 species across 16 genera. Ancestral area reconstructions were performed using PhyGeo, a geographically explicit, diffusion-based method that integrates species distributions with a dynamic palaeogeographic model applied to a pixelated spherical model of the Earth. Our analysis produced contrasting results depending on model assumptions. Under the Global Model, which treats all land features as equally habitable, Turdidae likely originated in West Antarctica-South America, with later colonization of Africa, Australia, and Asia via an Antarctic route. In contrast, the Restricted Model, which excludes unglaciated Antarctic land, shifted the inferred origin to northern North America, placing ancestral ranges closer to extant distributions and more consistent with current evidence. These results underscore the importance of considering multiple lines of evidence and spatially explicit approaches when reconstructing biogeographic histories.
The thread-legged bug tribe Leistarchini (Hemiptera: Reduviidae: Emesinae) is a cosmopolitan and diverse group characterized by a highly disproportionate spatial distribution across zoogeographic regions. Due to a historical lack of phylogenetic focus, the internal relationships and evolutionary history of the tribe remain poorly understood. In this study, we provide the first robust phylogenetic framework for Leistarchini by integrating molecular data from mitochondrial genomes and nuclear rDNA (88 taxa, 19 937 bp) with universal single-copy orthologs (24 taxa, 667 loci). Our results support the monophyly of Leistarchini and identify five major clades, including a newly described genus Calliemesa gen. n. Our findings further reveal that the five most species-rich genera (Nesita, Orthunga, Pleias, Ploiaria and Tinna) are either paraphyletic or polyphyletic as currently circumscribed. Molecular dating and biogeographic reconstructions suggest a Southeast Asian origin for the Leistarchini crown group during the late Palaeocene (ca. 57 Ma). Early diversification appears to have been driven by Paleogene geological and climatic shifts in Southeast Asia, while multiple intercontinental dispersals since the middle Eocene into the Afrotropics, Madagascar and the New World shaped the current global distribution. Ancestral state reconstructions indicate that the Leistarchini ancestor possessed a well-developed posterior pronotal lobe and a three-segmented protarsus. Subsequent evolutionary trajectories involved four independent transitions toward a shortened posterior pronotal lobe, and four separate reductions in protarsal segmentation.
Wheeler and Varón (2025) proposed phylogenetic minimum description length (PMDL) as a phylogenetic optimality criterion grounded in algorithmic (Kolmogorov) complexity. PMDL applies the minimum description length (MDL) principle to phylogenetic inference, but its claim that its graph complexity penalties arise 'naturally' and are 'not externally specified' merits careful interpretation. In MDL, description lengths are defined relative to a fixed description language, which can be interpreted as encoding domain-specific background assumptions that function analogously to implicit priors over hypotheses. In PMDL, this can be illustrated by the large graph complexity penalties assigned to phylogenetic networks, particularly the sharp increase when moving from a tree to a minimal network. These penalties reflect modelling assumptions rather than consequences determined by algorithmic complexity alone. Accordingly, PMDL's graph penalties are natural only in the conditional sense that they are not externally specified once a description language for phylogenetic graphs is fixed. The choice of that language, however, remains a substantive external modelling decision. While graph complexity provides the clearest illustration, the principle that description languages encode substantive modelling decisions also applies to PMDL's model complexity. Making this explicit clarifies the interpretation of PMDL within the MDL framework and renders its background assumptions open to evaluation.
Phylogenomics with abundant informative sites offers a powerful means for elucidating complex diversification history. Here, we collected 22 samples from 18 populations representing all species of subgenus Caloscordum (Allium). Using transcriptome and whole-genome resequencing data, we generated 1755 low-copy nuclear genes and 81 plastid genes. By integrating morphological and phylogenomic evidence, we clarified the subgenus's complex evolutionary histories and speciation patterns. A total of 18 morphological characteristics were analysed, with a taxonomic framework established. Our analyses resolved robust species relationships despite detecting extensive phylogenetic discordances, which were attributed to incomplete lineage sorting (ILS) and hybridization. Specifically, our results suggest that A. inutile originated via rapid budding speciation from the widespread A. tubiflorum. This process likely coincided with mid-Pleistocene glacial-interglacial cycles and may have been reinforced by geographic isolation and ecological adaptation. In contrast, the sole tetraploid species, A. peikingense, was confirmed to be of hybrid origin, derived from A. neriniflorum and A. tubiflorum. This allopolyploidization event appears to have been facilitated by secondary contact between the parent species, which was likely associated with climatic oscillations within the 35° N-45° N arid belt. Overall, our findings elucidate the intricate speciation patterns within Caloscordum and highlight how the interplay of polyploidization, ecological isolation, and tectonic uplift-driven aridification has shaped plant diversity in East Asia.
Toxodontidae represents a major extinct radiation of South American native ungulates, but persistent polytomies in morphological phylogenies have masked its evolutionary history. To address this, we perform a new combined-evidence phylogenetic analysis. We integrate a revised and dependency-coded matrix of 54 discrete characters with 42 morphogeometric and 5 continuous characters, across a comprehensive sample of 37 taxa. This approach overcomes key logical limitations of previous discrete datasets and quantitatively captures shape variation. The analysis yields a fully resolved and well-supported topology for Toxodontidae, with Adinotherium, Proadinotherium and Nesodon forming a paraphyletic assemblage. We identify five major clades, several of which are strongly supported and formally define them based on their sister-group relationships: Xotodontinae is sister of Altiplaniinae, both are sister to a clade comprising Haplodontheriinae and Mixodontinae + Toxodontinae. Branch length decomposition shows the initial divergence and key internal nodes were dominated by discrete character change, while later radiations were driven by morphogeometric change, indicating diversification through shape reorganization. Ancestral reconstructions reveal a shift from a generalized morphotype to specialized forms with euhypsodonty, incisor hypertrophy and larger dental dimensions. This robust phylogenetic framework resolves the long-standing impasse within Toxodontidae phylogeny and provides a foundation for testing evolutionary and biogeographic hypotheses.
