The Madras hedgehog (Paraechinus nudiventris) is an understudied species endemic to southern India, with limited genetic data available for understanding its evolutionary history. Here, we present the complete mitochondrial genome (17,232 bp), annotated and analysed in comparison with other Erinaceidae species. The mitogenome retains the typical vertebrate structure, comprising 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region, with an A + T rich nucleotide composition. Phylogenetic analyses using Bayesian and maximum-likelihood approaches confirmed the species’ placement within Paraechinus, with divergence from P. micropus estimated during the Pleistocene. Molecular evolutionary analyses revealed selective constraints on oxidative phosphorylation genes, with atp8 showing the highest variability. Our divergence time estimates, incorporating fossil calibrations, refine the evolutionary timeline of Erinaceidae, providing insights into the diversification of hedgehogs in South Asia. By making this annotated mitochondrial genome publicly available, we provide a foundational resource for future studies on the genetic diversity, phylogeography, and conservation of P. nudiventris and its relatives.

The Ediacaran Weng'an Biota of South China yields embryo-like microfossils preserved with sub-cellular fidelity, previously interpreted as the oldest evidence of animals. Megasphaera dominates the assemblage and preserves the earliest stages of binary reductive division. It is assumed to develop into Megaclonophycus, which is composed of hundreds to thousands of cells; however, this developmental link has not been tested. We used synchrotron and computed tomography to characterize hundreds of specimens of Megaclonophycus and determine cell division patterns. Specimen cell counts range from 14 to 10 201, with counts clustering around 2048 and 4096, consistent with binary reductive cell division. However, the specimens have asynchronous binary cell division with cell sizes within a specimen varying by two- to threefold. The volume of Megaclonophycus is variable during development, showing no evidence of gastrulation, characteristic of metazoan development. Megaclonophycus and Megasphaera exhibit a similar sequence of development, size and taphonomy indicating a developmental sequence of early to later stages of the same organism. These findings are incompatible with the crown group metazoan affinity suggested for this taxon, and so molecular clock estimates for the origin of animals must rely on fossil calibration from sources other than Megaclonophycus.

ABSTRACT Aim Protecting phylogenetic diversity (PD) has been advocated as a basis for spatial conservation planning. However, phylogenetic branch lengths can vary substantially depending on methodological choices made during the inference of phylogeny and divergence times, and little is known about the sensitivity of spatial patterns of PD to these choices. We aimed to test the variability of spatial PD patterns, including the size and locations of ‘hotspots’ of evolutionary history, under alternative phylogenetic methods. We then aimed to test the downstream effects for conservation priority areas selected using Systematic Conservation Planning methods. Location Australia. Methods Using phylogenomic and fossil data for the plant clade Grevilleoideae (663 species), we inferred divergence times under 26 combinations of methods relating to topology and divergence time estimation, choice of fossil calibration, calibration constraints, and evolutionary model parameterization. We compared spatial patterns of PD and conservation priority areas selected using a reserve selection algorithm across the resulting 26 phylogeny treatments. Results Continent‐wide, there was substantial incongruence in spatial PD patterns among treatments, with large areas identified as PD hotspots or priority areas under fewer than 26 treatments. Areas of incongruence in priority areas amounted to approximately 30% of the land budget allocated to expansion of the protected area network in our simulations (~8% of Australia's land area). Spatial patterns were especially sensitive to the choice of Bayesian (MCMCtree) vs. fast rate‐smoothing (RelTime) methods of divergence dating. Main Conclusions Spatial patterns of PD and choice of priority areas for conservation of PD can vary substantially under alternative, routine, methodological choices in phylogenetics. This introduces uncertainty into conservation planning that aims to maximize protection of evolutionary history. Uncritical use of phylogenetic information in conservation may lead to wasted resources or poor conservation outcomes.

Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing representatives of clades that far pre-date the age of the clade inferred using phylogenies built from molecular data and previous fossil calibrations. Recently, one fossil with the potential to drastically change current understanding surrounding the timescale of reptile diversification was described from Triassic fissure-fill deposits in the United Kingdom. This taxon, †Cryptovaranoides microlanius, was originally placed deep within the squamate crown clade, suggesting that many lineages of living lizards and snakes must have appeared by the Triassic and implying long ghost lineages that paleontologists and molecular phylogeneticists have failed to detect using all other available data. Our team challenged this identification and instead suggested †Cryptovaranoides had unclear affinities to living reptiles, but a crown-squamate interpretation was later re-iterated by the team that originally described this species. Here, we again challenge the morphological character codings used to support a crown squamate affinity for †Cryptovaranoides microlanius and illustrate several empirical problems with analyses that find this taxon is a crown squamate. Our analyses emphasize the importance of stringency in constructing hypodigms of fossils, particularly when they may be key for proper time calibration of the Tree of Life.

Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing representatives of clades that far pre-date the age of the clade inferred using phylogenies built from molecular data and previous fossil calibrations. Recently, one fossil with the potential to drastically change current understanding surrounding the timescale of reptile diversification was described from Triassic fissure-fill deposits in the United Kingdom. This taxon, †Cryptovaranoides microlanius, was originally placed deep within the squamate crown clade, suggesting that many lineages of living lizards and snakes must have appeared by the Triassic and implying long ghost lineages that paleontologists and molecular phylogeneticists have failed to detect using all other available data. Our team challenged this identification and instead suggested †Cryptovaranoides had unclear affinities to living reptiles, but a crown-squamate interpretation was later re-iterated by the team that originally described this species. Here, we again challenge the morphological character codings used to support a crown squamate affinity for †Cryptovaranoides microlanius and illustrate several empirical problems with analyses that find this taxon is a crown squamate. Our analyses emphasize the importance of stringency in constructing hypodigms of fossils, particularly when they may be key for proper time calibration of the Tree of Life.

Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing representatives of clades that far pre-date the age of the clade inferred using phylogenies built from molecular data and previous fossil calibrations. Recently, one fossil with the potential to drastically change current understanding surrounding the timescale of reptile diversification was described from Triassic fissure-fill deposits in the United Kingdom. This taxon, † Cryptovaranoides microlanius , was originally placed deep within the squamate crown clade, suggesting that many lineages of living lizards and snakes must have appeared by the Triassic and implying long ghost lineages that paleontologists and molecular phylogeneticists have failed to detect using all other available data. Our team challenged this identification and instead suggested † Cryptovaranoides had unclear affinities to living reptiles, but a crown-squamate interpretation was later re-iterated by the team that originally described this species. Here, we again challenge the morphological character codings used to support a crown squamate affinity for † Cryptovaranoides microlanius and illustrate several empirical problems with analyses that find this taxon is a crown squamate. Our analyses emphasize the importance of stringency in constructing hypodigms of fossils, particularly when they may be key for proper time calibration of the Tree of Life.

ABSTRACT Aim African freshwater fishes serve as important biogeographical indicators of geomorphological and hydrological history across the continent. However, research focusing on the phylogeny, biogeography and diversification of African fishes, particularly in central Africa, is relatively scarce. Here, we evaluate three geological hypotheses regarding the formation of the contemporary Congo basin: (1) the dominance of the Ogooué and Kouilou rivers along the western continental margin during the Cretaceous, (2) an eastward‐flowing Congo‐Zambezian system forming the Rufiji Delta during the Paleogene and (3) river basin capture resulting in the formation of the Lower Congo River during the Pliocene. To do this, we reconstructed the phylogeny of featherfin tetras of the genus Bryconaethiops using their mitochondrial genomes, estimated diversification chronology, and detected biogeographic transitions in Central Africa. Location Afrotropical rivers of Nilo‐Sudan, Lower Guinea, Congo and Malagarasi‐Tanganyika. Time Period Oligocene, Neogene and Quaternary. Taxon Bryconaethiops (Teleostei: Characiformes: Alestidae). Methods Analysis of a molecular matrix of complete mitochondrial genomes comprising 13 protein‐coding genes totaling 14,869 bp for 36 Bryconaethiops and related alestid taxa. Phylogenetic analyses included maximum likelihood, Bayesian fossil calibration, and parametric biogeographic reconstructions. Support for generic monophyly was evaluated using internal and external anatomy with microcomputed tomography (μCT) and conventional morphometric/meristic analyses. Data from museum specimens provided updated distributional ranges for each Bryconaethiops species. Results Time‐calibrated phylogenetic and biogeographic analyses suggest initial diversification of Bryconaethiops occurred in Lower Guinea during the Oligocene ( ca. 25 Ma), followed by transitions to the Nilo‐Sudan and Middle Congo regions during the Early Miocene ( ca. 19–17 Ma). Three distinct Pleistocene dispersal events to the Lower Congo ( ca. 0.7–0.05 Ma) and three to the Upper Congo and Malagarasi of Tanganyika ( ca. 1.5–0.1 Ma) were detected. Morphological analysis reveals four generic synapomorphies associated with modification of the upper and lower jaws, dentition and elongation of dorsal‐fin lepidotrichia, in addition to evidence for revalidation of B. mocquardianus (Thominot, 1886) from Atlantic coastal rivers of the eastern Gulf of Guinea. Main Conclusions Genetic and biogeographical analysis of Bryconaethiops supports the hypothesis that an expansive, centrally situated lowland proto‐Congo was captured by the modern Lower Congo during the Plio‐Pleistocene. Sympatric occurrences of sister taxa point to a complex scenario of allopatric speciation followed by secondary contact and/or resource partitioning across the Congo basin.

MCMCtree and r8s are among the most popular molecular dating tools in the current genomic era, but their utility is hampered by steep learning curves, particularly concerning input file formatting, the complexity of fossil calibration setup, tree visualization, and model selection. To enhance their usability and improve research efficiency, we developed three new tools: MDGUI (for molecular dating analysis), TimeTreeAnno (for timetree visualization), and MCMCTracer (for convergence assessment). We integrated these into the PhyloSuite v2 platform, along with MCMCtree and r8s plugins, to create a comprehensive molecular dating suite. Compared to existing solutions that we benchmarked, our toolkit offers a more intuitive interface and streamlined workflow, featuring visual calibration point configuration, support for multiple alignment formats, automated model selection and implementation for downstream analyses, one‐click pause/resume functionality, multithreading acceleration, and on‐demand MCMC convergence assessment and plotting. Furthermore, PhyloSuite v2 introduces other advanced features, including gene duplicate resolution during the extraction step, significantly accelerated data handling capabilities (specifically, format conversion and concatenation), deeper integration of the latest IQ‐TREE models and functions, and further streamlining of the entire phylogenetic analysis workflow. The update also includes adaptation to high‐resolution screens and numerous bug fixes. The source code for the new version of PhyloSuite is available at https://github.com/dongzhang0725/PhyloSuite.

The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling > 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the "fast" maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a "divide-and-conquer" strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a dataset that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight the advantages of recently developed fast tree search approaches initiated with parsimony starting trees, which offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies.

ABSTRACT Aim We examine biogeography and speciation patterns in Miliusa Lesch. ex A. DC. (~65 species) distributed in tropical Asia to understand the uneven distribution of its extant diversity, with Indo‐Burma having twice the species richness of peninsular India (PI) and four times that of Wallacea and Sahul. Location Tropical Asia. Taxon Miliusa (Annonaceae). Methods Phylogenetic reconstruction was performed using six plastid markers across fifty‐two species using both ML and BI approaches. Divergence times were estimated using two fossil calibrations and an optimized relaxed clock, and ancestral areas were inferred with ‘BioGeoBEARS’. Speciation rates were examined using ClaDS and the DR statistic, and community structure was assessed using phylogenetic diversity metrics. Results Miliusa likely originated in the mid‐Miocene, with Indo‐Burma and PI as its ancestral range. Its extant diversity is primarily attributed to in‐situ speciation, with dispersal or vicariance playing limited but important roles in PI, and Wallacea and Sahul. Lineages in Indo‐Burma began accumulating in the mid‐Miocene, preceding those in PI (~10 Myr) and Wallacea and Sahul (~5 Myr). PI showed signs of saturation in lineage accumulation and had lower speciation rates compared to Wallacea and Sahul and Indo‐Burma, both of which had similar rates. All regions exhibited phylogenetic clustering, but Indo‐Burma and PI differed in their sensitivity to phylogenetic depths. Main Conclusions The uneven diversity of Miliusa is shaped by time for speciation, age and dispersal, although their relative influence varies across regions. In Indo‐Burma, long‐term geo‐climatic stability and greater niche availability likely facilitated the persistence of lineages, rapid speciation and dispersal, making it an evolutionary hotspot for Miliusa . In contrast, PI exhibited lower richness and speciation rates despite being old, likely due to the contraction of wet habitats in the Miocene that limited available niches for speciation. Lineages in Wallacea and Sahul show typical island‐like radiations, with speciation rates comparable to the larger and more geo‐climatically stable Indo‐Burma, despite their more recent origin. Overall, our results highlight the role of Miocene‐driven climatic vicariance and Pliocene–Pleistocene climatic fluctuations in shaping the diversification dynamics and regional diversity patterns across tropical Asia.

Despite their relevance as model organisms, the early diversification patterns in Drosophilidae remain poorly resolved, with most studies focusing on Drosophila. Here, we employed a phylogenomic framework for 33 taxa: 27 drosophilid species representing most tribes of both subfamilies (Drosophilinae and Steganinae) plus 6 taxa from other families of Ephydroidea (Braulidae, Cryptochetidae, Curtonotidae, and Ephydridae). Besides inferring phylogenetic relationships, we estimated divergence times and substitution rates using a fossil-calibrated Bayesian approach. Our results recover Drosophilinae as monophyletic (among the taxa sampled) but place Braula coeca (Braulidae) within Steganinae, rendering Drosophilidae nonmonophyletic and underscoring the need for taxonomic revision. Relationships within Steganinae (including Braula) were fully resolved, whereas the position of some Drosophilinae lineages (eg Scaptodrosophila) remains uncertain, likely due to extensive gene tree heterogeneity. Divergence time estimates suggest that the family originated near the Cretaceous–Paleogene boundary (67.3 Ma; 95% highest posterior density: 83 to 52 Ma), with subfamilies diversifying primarily during the Eocene (56 to 34 Ma). The neutral evolutionary rate, estimated from fossil calibrations and third codon positions, aligns with previous biogeographically calibrated estimates but is lower than mutation-derived rates, likely reflecting the action of purifying selection and uncertainty about generation times across lineages.

Abstract Meiogyne is a genus of shrubs, trees and treelets occurring in India, tropical Southeast Asia, and Australasia–Pacific, an unusually wide distribution across Australasia and the Western Pacific compared to other genera of Annonaceae. Previous chloroplast phylogenies of the genus offered poor resolution and support. Here, a molecular phylogeny was reconstructed based on 27 described Meiogyne species (ca. 70% sampling) using seven chloroplast and 11 nuclear markers. The combined data set generated a well‐resolved and well‐supported phylogeny. Estimation of divergence time utilized two fossil calibrations and an uncorrelated log‐normal relaxed clock model. Trait‐dependent and trait‐independent biogeographical models in BioGeoBEARS were compared using corrected Akaike information criterion weight and the likelihood ratio test. The results suggest that narrow monocarp width is correlated with increased macroevolutionary dispersal. Under the best‐fitting trait‐dependent DEC + j + t12 + t21 + m2 model, a single colonization event from Sunda to Sahul during the middle Miocene and two dispersal events from New Guinea and Australia into the Pacific during the late Miocene to early Pliocene were detected. BayesTraits analysis strongly supports a correlation between narrow monocarp width and bright fruit colors. Bird dispersal and the associated traits (narrow monocarp width) may have driven macroevolutionary dispersal for Meiogyne in Australasia–Pacific.

Dating the tree of Fungi has been challenging due to a paucity of fossil calibrations and high taxonomic diversity of the group. Here we reconstructed and dated a comprehensive phylogeny comprising 110 fungal species, utilizing 225 phylogenetic markers and accounting for across-site compositional heterogeneity in amino acid sequences. To address uncertainties in fungal dating, we sampled chronograms from four relaxed molecular clock analyses, each integrating distinct sets of calibrations and relative time-order constraints. The first analysis used a core set of 27 calibrations alongside 17 relative constraints derived from fungi-to-fungi horizontal gene transfer events. Three further analyses extended this core set with additional timing information identified in our reevaluation of the evolution of pectin-specific enzymes in Fungi. Our timetree, integrating analytic uncertainties, suggests older ages for crown Fungi (1,401-896 Ma) than recently reported, providing a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253-797 Ma). This supports a protracted gap between the onset of these interactions and the rise of modern land plants. Altogether, our study provides a refined timescale for fungal diversification and a temporal framework for future investigations into early interactions involving fungi and the algal ancestors of embryophytes.

SummaryStoneflies (order Plecoptera), one of the earliest winged insects, are ecologically vital as freshwater bioindicators. Despite their ecological and evolutionary significance, a robust phylogeny for stoneflies has remained elusive. Here, we analyzed mitogenomes from 97 species representing all 17 families, employing site-heterogeneous models to reconstruct a comprehensive phylogeny of global Plecoptera. Our results provide several key insights: 1) Scopuridae is the earliest diverging lineage within Euholognatha; 2) Taeniopterygidae and Leuctridae form sister groups, representing the second diverging clade within Euholognatha; 3) Capniidae is resolved as the sister group to Nemouridae + Notonemouridae; and 4) the phylogenetic relationships within Systellognatha are resolved. Furthermore, by integrating palaeontological and chronostratigraphic data, we selected well-vetted fossil calibrations to reconstruct a temporal framework for Plecoptera evolution. Our study identifies key periods in Plecoptera’s early divergence and the origins of extant stonefly families, establishing a foundation for future research into their biogeography, morphology, and behavioral evolution.

Reproductive isolation and genomic divergence both accumulate over time in the formation and persistence of distinct biological species. The pace of “speciation clocks” quantified with pre-zygotic and post-zygotic reproductive isolation, however, differs among taxa, with pre-zygotic isolation tending to evolve sooner in some but not all taxa. To address this issue in nematodes for the first time, here we infer the species tree and divergence times across the phylogeny of 51 species of Caenorhabditis. We incorporate several molecular evolutionary strategies in phylogenomic dating to account for complications in this group due to lack of fossil calibration, deep molecular divergence with synonymous-site saturation, and codon usage bias. By integrating divergence times with experimental data on pre- and post-zygotic reproductive isolation, we infer that post-zygotic isolation accumulates faster than pre-zygotic isolation in Caenorhabditis and that hybrid sterility evolves sooner than hybrid inviability. These findings are consistent with speciation being driven principally by intrinsic isolating barriers and the disproportionate fragility of germline developmental programs to disruption. We estimate that it takes approximately 50 million generations for intrinsic post-zygotic reproductive compatibility to be reduced by half, on average, between diverging pairs of Caenorhabditis. The protracted reproductive isolation clocks in Caenorhabditis may, in part, reflect the capacity to retain population genetic hyperdiversity, the incomplete sampling of global biodiversity, and as-yet uncharacterized incipient or cryptic species.

Hemiptera, the fifth most diverse insect order, are characterized by their high diversity in deep time, with 145 known extinct families. However, the precise timing of the origin of Hemiptera lineages has remained uncertain. Traditional approaches, molecular clock analyses and fossil calibrations, have overlooked much of this extinct diversity by failing to incorporate key fossil data. Furthermore, no estimates have been proposed for the timing of the extinction of Hemiptera’s fossil lineages. In this study, we use the recently developed Bayesian Brownian Bridge model, which estimates the timing of lineage origin and extinction through fossil-based Bayesian modelling, to provide a temporal framework for the rise and fall of 310 major hemipteran lineages. Our results support an early Pennsylvanian origin of Hemiptera, and indicate that the major hemipteran lineages originated between the late Carboniferous and Late Permian (Pennsylvanian-Lopingian). Additionally, our analyses reveal a radiation of Hemiptera during the Permian (Guadalupian), followed by multiple extinctions of ancient hemipteran lineages from the Permo-Triassic boundary to the mid-Triassic. A second major radiation occurred during the Cretaceous, coinciding with numerous extinctions of relic and newly emerging Cretaceous lineages, highlighting a faunal turnover. Our study provides a holistic fossil-based picture of the evolutionary history of Hemiptera.

Molecular phylogenetics elucidates the evolution and divergence of green plants by analyzing sequence data from diverse sources. Notably, phylogenetic reconstruction based on mitochondrial genes often shows incongruence with results from nuclear and chloroplast genes. Although the uniparental inheritance and conservatively retained protein-coding genes of mitochondrial genomes inherently exclude certain confounding factors that affect phylogenetic reconstruction—such as hybridization and gene loss—the use of mitochondrial genomes for phylogeny and divergence-time estimation has remained limited. Here, we assembled a comprehensive dataset of 565 mitochondrial genomes representing all major lineages of green plants. Applying multiple partitions and phylogenetic models, our mitochondrial-based phylogenies support paraphyly in both bryophytes and charophytes, place hornworts (Anthocerotaceae) as sister to all tracheophytes, and recover stoneworts (Charophyceae) as sister to land plants. We systematically evaluated the influence of factors in mitochondrial coding sequences, including GC-content heterogeneity and codon-usage bias. Furthermore, by rigorously testing seven dating strategies, we assessed the impact of confounding elements affecting divergence-time estimates, such as fossil calibration number and prior settings, as well as rate heterogeneity among sites and across lineages. Our dating analyses support a Neoproterozoic origin (crown age) of land plants and a Triassic origin of angiosperms, consistent with nuclear evidence. In conclusion, we emphasize the importance of exploring alternative partitioning strategies and addressing among-lineage heterogeneity in both phylogenetic and dating analyses, with extended sampling and careful data pruning to minimize systematic error in phylogenetic inference.

Molecular data are irreplaceable resources for reconstructing the tree of life. Gene-specific substitution rates are essential for estimating divergence times in the absence of fossil calibration or converting coalescent units into absolute time in phylogeographic approaches, among other uses. However, substitution rate estimates are often derived from limited genomic loci, narrow taxonomic comparisons, and model organisms, hindering their applicability to understudied taxa. Among mammals, bats (Order Chiroptera)-despite their ecological diversity and evolutionary significance-remain underrepresented in substitution rate studies, particularly within the family Vespertilionidae, the third largest mammal family. Here, we investigate mitochondrial genome (mitogenome) evolutionary rates in this group, while also describing the first complete mitogenomes of three Neoeptesicus species: N. brasiliensis, N. diminutus, and N. furinalis. Using fossil-calibrated Bayesian phylogenetic analyses, we estimated that protein-coding genes evolve at rates between 0.0055-0.0089 substitutions per site per million years (subs/site/Ma), while ribosomal RNA genes evolve at rates between 0.0035-0.0049 subs/site/Ma. Notably, the ND4, ND4L, and ND5 genes exhibited the highest rates, whereas non-coding regions showed the lowest, suggesting that gene-specific evolutionary constraints influence these rates. These findings provide the first comprehensive substitution rate framework for Vespertilionidae mitogenomes, addressing a critical gap in genomic resources for this taxonomically complex group. By integrating novel mitogenomic data with rigorous rate estimation, this study advances our capacity to resolve evolutionary patterns in bats, offering a benchmark for future phylogenetic and phylogeographic studies in non-model mammals.

Abstract The tribe Cunonieae comprises five genera and 214 species of shrubs and trees currently distributed in the Southern Hemisphere and the tropics, exhibiting an amphi‐Pacific disjunct distribution shared with Araucariaceae, Myrtaceae, Nothofagaceae, Podocarpaceae, and Proteaceae, among others. To address the central question of how historical geological forces have shaped the distribution of plant diversity in the southern hemisphere, we aimed to provide evidence from the biogeographical history of Cunonieae. We generated the most densely sampled phylogenetic trees of Cunonieae available to date, with 121 samples and 81 species, based on 404 new sequences of plastid and nuclear DNA regions with high hierarchical phylogenetic signal (matK, trnL‐F, rpl16, and internal transcribed spacer (ITS)). We included 184 samples of Rosids to estimate divergence times using fossil calibration points. For biogeographic inference, we employed a time‐stratified model including fossils as tips. Cunonia and Pterophylla were paraphyletic in the ITS tree, and Cunonia was paraphyletic in the plastid tree. Pancheria, Vesselowskya, and Weinmannia were monophyletic, the latter with conflicting nuclear and plastid phylogenies. The crown group Cunonieae was dated at ~56 Ma, and its ancestral areas were Antarctica and Patagonia. Antarctica acted as a bridge between Australia and South America before the consolidation of the Antarctic Ice Sheet and the extinction of the lineage in Antarctica from the Oligocene to the Miocene. Following that, Cunonieae spread to lower latitudes via Zealandia/Oceania and Patagonia/South America. Geological changes during the Pliocene facilitated a further burst in diversification along the Andes, in Madagascar, and in New Caledonia, where at least three colonization events occurred.

ABSTRACTAimTo infer the biogeographic history of the Triatomini by evaluating how their species became part of the biogeographic transition zones of the New World. This group of blood‐feeding insects includes key vectors of Chagas disease. Understanding their dispersal and diversification over geological time may help elucidate the temporal dynamics of faunal assembly during the colonisation of different areas across the continent.LocationAmericas.TaxonTriatomini kissing bugs.MethodsWe analysed 70 published UCE data of 55 Triatomini terminals, which belong to 39 of its 113 described species. We conducted partitioned ML analyses to reconstruct the phylogenetic relationships within the group. We then estimated the divergence times using one fossil calibration point. With the resulting chronogram, we inferred the ancestral geographic ranges associated with internal nodes of the phylogeny using BBM and BAYAREALIKE + J models.ResultsThe most likely ancestral range for the crown node of Triatomini is the Neotropical–South American + South American Transition Zone (SATZ), suggesting that the tribe originated as part of the South American biota during the Oligocene–Miocene, in temporal association with the orogenic uplift of the Andes. A single dispersal to North America was inferred during the Miocene, initially reaching Mesoamerica and subsequently expanding into the Mexican Transition Zone (MTZ) and the Nearctic region, at a time when the Mexican Plateau had reached an advanced stage of geological evolution.Main ConclusionOur study challenges the expectations derived from the cenocron framework proposed for the Mexican Transition Zone, which assumes multiple independent colonisation events. Instead, our results are more consistent with an Ancient Neotropical distribution pattern, in which South American ancestors reached the MTZ during the Oligocene–Miocene through a single dispersal process that contributed to the current faunal assembly.