Fabien L. Condamine

Summary: Whether evolutionary radiations are primarily driven by ecological or neutral processes remains an unresolved question. The karst‐endemic genus Petrocodon , distributed across southern China and northern Indochina, provides a powerful system for testing these alternatives. We generated whole‐genome sequencing data for 54 of the 60 described species and integrated these with morphological, geographic, and paleoclimatic data to evaluate the relative roles of ecological and neutral processes in diversification. Our analyses revealed a robust nuclear phylogeny but extensive cytonuclear discordance, likely due to pervasive ancient hybridization and introgression. Macroevolutionary and biogeographic analyses indicate that diversification began during a favorable climatic period enabling range expansion, but subsequent species accumulation was primarily driven by geographic isolation and allopatric divergence rather than ecological niche differentiation. Morphological evolution decoupled from lineage diversification, with most morphological diversity accumulating relatively late. Further analyses support genetic drift in small, isolated populations driving morphological evolution, although stabilizing selection cannot be excluded, and reticulate evolution may have additionally contributed to phenotypic innovation. Together, these results support a largely nonadaptive radiation in Petrocodon , in which spatial opportunity played a central role in species accumulation, while demographic and reticulate processes may have contributed to its striking phenotypic diversity.

Species richness varies widely among taxonomic groups, and understanding the drivers of these disparities remains a key challenge. Using the most recent time-calibrated phylogeny of Caudata (763 species), we investigated how abiotic and biotic factors shape diversification in this amphibian clade, known for its ecological and life-history diversity. We first assessed the respective roles of clade age and diversification rates in explaining species richness using two branch-specific models. We then tested the influence of past temperature, continental fragmentation, and life cycle on diversification using environment- and state-dependent models. Our results show that diversification rates, rather than clade age, primarily explain richness differences. High speciation rates are found in young lineages and in early branches of the three most diverse families, suggesting early radiations followed by slowdowns. Likelihood-based analyses further suggest a positive association between temperature fluctuations and diversification. Weak temperature effects in Plethodontidae and absence of effect in Salamandridae and Hynobiidae point to lineage-specific dynamics. However, Bayesian inference-based models failed to recover reliable diversification dynamics, likely reflecting the inherent difficulty of estimating time-varying speciation and extinction rates from this phylogeny. Consequently, the precise temporal trajectory of diversification and the causal interpretation of environmental associations remain uncertain. State-dependent models show no significant effect of life cycle. Instead, other traits likely drive diversification patterns. Together, our findings highlight the central role of diversification rate heterogeneity in shaping species richness disparity, and the challenges of disentangling the macroevolutionary processes driving salamander evolutionary history.

Underlying diversification patterns and potential drivers of land plants remain puzzling, particularly at deep-time and global scales. Here, we reconstruct the diversification dynamics of land plants using an updated time-calibrated phylogeny comprising approximately 30,000 extant species, and nearly 40,000 fossil occurrences within the Bayesian birth-death frameworks. Our analyses indicate that angiosperms exhibit the highest diversification rates, whereas ferns underwent a marked diversification increase during the Cretaceous, coincident with the rapid radiation of angiosperms. Among the major Phanerozoic mass extinctions, the Cretaceous-Paleogene event has the most significant impact on land plant diversity, with estimated genus-level losses of 13%, 14%, and 4% in bryophytes, pteridophytes, and gymnosperms. We identify a pattern consistent with competitive displacement scenario, in which pteridophytes origination rates declined as gymnosperm diversity increased, accompanying the transition from pteridophyte- to gymnosperm-dominated floras. We find that plant-insect interactions have originated as early as the emergence of pteridophytes, potentially promoting the diversification of pteridophytes and gymnosperms. During the Cretaceous, these associations shifted toward angiosperms, as indicated by a positive relationship between insect diversity and angiosperm origination rates. Finally, continental fragmentation, fluctuations in aridity, atmospheric carbon and sedimentary dynamics, showed stronger associations with the successive rise and decline of major land plant groups.

Tropical rain forest is the most diverse terrestrial biome, yet the drivers of its diversification across space and time remain poorly understood. Although heterogeneous diversification rates, including both ancient and recent radiations, have been reported, these dynamics have rarely been examined within a single lineage across deep evolutionary timescales. Here, we reconstruct a dated phylogenomic tree of the pantropical plant family Annonaceae, sampling 2045 species (∼82% of its diversity) and spanning ∼100 million years of evolutionary history. Diversification dynamics vary markedly across tropical regions, correlated with distinct environmental factors rather than uniform processes. Sea level fluctuations dominate in the Asia-Pacific, whereas paleotemperature shapes diversification in the Afrotropics and Neotropics. We also detect a Late Cretaceous increase in diversification, indicating that a substantial portion of Annonaceae diversity originated before the Cretaceous-Paleogene boundary. Together, these results highlight how regional environmental trajectories have shaped the assembly of a diverse tropical plant family over deep evolutionary time.

Diving beetles (Dytiscidae) constitute the most successful radiation of aquatic beetles, exhibiting a near‐global distribution and ecological diversity. Yet, the historical biogeography of the family and the determinants of biogeographic range size across lineages remain poorly understood, largely due to past phylogenetic uncertainties and the lack of an integrative macroevolutionary framework. Here, we address these gaps by inferring a genus‐level phylogeny of Dytiscidae, sampling ~76% of the described genera and integrating molecular data with recent phylogenomic constraints and time calibrations. We estimate divergence times using Bayesian relaxed clock approaches and ancestral ranges under a maximum‐likelihood time‐stratified biogeographic model. We also investigate the drivers of biogeographic range size using phylogenetic comparative methods, focusing on habitat type, niche breadth, body size and diversification rates. Our results provide a global dated framework for Dytiscidae, supporting an origin in the Nearctic or the Nearctic + Neotropics during the Late Triassic (~210 Mya). Furthermore, Antarctica may have played a transitional role in shaping Australasian diversity through past palaeogeographic connectivity, although this hypothesis remains tentative as no extant species live in this region. Comparative analyses indicate that habitat type and niche breadth are associated with variation in range size, although they explain only a small portion of that variation. Body size shows no detectable effect, whereas diversification rates display a positive association with range size. Overall, these results suggest that the distribution of Dytiscidae reflects the interplay between historical contingencies and ecological factors while underscoring the importance of methodological uncertainty when linking macroevolutionary dynamics to spatial patterns.

With the massive increase in genomic resources, it is becoming increasingly popular to analyse thousands of loci across many species. However, many of the available genomes are not annotated, which hinders an efficient search for orthologous protein‐coding genes. Here, we aim to develop a semi‐automated pipeline and compare four genomic annotation methods (BRAKER2, BUSCO, Miniprot and Scipio). Our results highlight the importance of integrating multiple annotation tools to optimise ortholog detection and improve genomic studies. Each annotation method showed different strengths. BRAKER2 annotated a substantial number of genes. BUSCO, despite limitations inherent to its reference database, identified a higher number of orthologs. Miniprot exhibited notable flexibility in accommodating diverse protein datasets, whereas Scipio successfully recovered a considerable set of genes that were not detected by the other tools. The combination of these tools allowed for more comprehensive ortholog detection. Taking advantage of this pipeline, we developed a comprehensive dataset of orthologous genes for swallowtail butterflies (Lepidoptera: Papilionidae), called Papilionidae_odb , which will facilitate future studies, especially for a non‐model group with abundant genomic data and few transcriptomic resources. We tested Papilionidae_odb by inferring a robust phylogenetic framework for Leptocircini using 142 complete genomes, which improved branch support for some phylogenetic relationships, although challenges remained in resolving relationships within certain species groups, likely due to rapid radiations. Our results highlight the complementary nature of the annotation methods and suggest that combining these tools can yield more accurate results in genomic research. This approach was implemented in a Snakemake workflow called CASIO (Combining Annotation Software to Identify Orthologous genes) and can easily be applied to other non‐model groups to improve genomic datasets in diverse taxa where transcriptomic resources are still limited.

Aim: Differences in the functional traits of co‐occurring species drive species' interactions and sustain key ecosystem services. However, the historical and contemporary environmental drivers of, as well as the surrogacy of conventional range‐based diversity metrics for, this functional diversity remain poorly understood. Here, we assess the drivers and spatial congruence of species richness, range rarity, and a major component of the global functional diversity of swallowtail butterflies—the body size and colour lightness dispersion—grounded in global‐scale analyses of their ecophysiological functions. Location: Global. Time Period: Contemporary. Major Taxa Studied: Papilionidae (Lepidoptera). Methods: Using comprehensive distribution data and two ecologically important and ubiquitous traits, namely body size and colour lightness, for 511 (80%) species, we examined the environmental drivers of assemblage‐level trait means and dispersion. Using trend surface models that account for environmental drivers, we further assessed the potential contribution of latent biogeographical drivers. Results: Species richness and range rarity, but not functional dispersion, decreased with latitude ( R ² = 34 > 21 > 5%), mainly due to similar effects of temperature and productivity. Hotspots of over‐dispersion uniquely highlighted Indomalaya and adjacent regions, while being largely absent from the Neotropic and Afrotropic. Being weakly driven by contemporary environmental factors, this pattern was even more prominent in the residuals explained by a latent, strongly longitudinally structured driver. Main Conclusions: The idiosyncratic relationships with environmental drivers and moderate congruence with conventional diversity measures suggest broad complementarity of functional dispersion. Notably, although environmental drivers strongly shape mean body size and colour lightness, consistent with ecophysiological mechanisms, they do not translate into filters of trait dispersion. Thus, while both traits are highly scalable and have a broad range of ecologically important functions, our results suggest that a complex interplay of ecological and evolutionary processes underpins large‐scale patterns in functional assemblage structure.

Wild silkmoths (Saturniidae) are one of the most emblematic and well-studied families of moths. Yet, the absence of a robust phylogenetic framework based on a comprehensive taxonomic sampling impedes our understanding of their evolutionary history. We sequenced and analyzed 1024 ultraconserved elements (UCEs) and their flanking regions to infer the relationships among 338 species of Saturniidae representing all described subfamilies, tribes, and genera. We investigated systematic biases in genomic data and performed dating and historical biogeographic analyses using extinction-free and state-dependent speciation and extinction models to document the evolutionary history of wild silkmoths in space and time. Using gene genealogy interrogation, we showed that saturation of nucleotide sequence data blurs our understanding of early divergences and first biogeographic events. Our results support a Neotropical origin of saturniids but remain inconclusive with respect to the extent of the ancestral range for the family. The “traditional” hypothesis of an origin restricted to the Neotropics is supported by models that account for founder-effect dispersal, but a new alternative scenario recovered from other models is proposed and considered a better fit to the hypothetical modes of diversification in these moths. It estimates a broader ancestral range covering the Neotropical, West Nearctic, and East Palearctic bioregions and emphasizes the critical role of Beringia as a route between the New World and the Old World during the Eocene. Interestingly, all the early branching lineages of Saturniidae that diversified into today’s recognized subfamilies are characterized by a very strong geographic conservatism, except for one noticeable exception, the Saturniinae subfamily, that is now present on all continents but Antarctica. Overall, our results provide a framework for in-depth investigations into the spatial and temporal dynamics of all saturniid lineages and for the integration of their evolutionary history into further global studies of biodiversity and conservation. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the proper alignment of taxonomic divisions and ranks with our phylogenetic results leads us to propose substantial rearrangements of the family classification, including the description of one new subfamily and two new tribes.

Whole‐genome sequencing has transformed our capacity to study population structure, define taxonomic boundaries and evaluate evolutionary and conservation processes. By capturing genome‐wide variation, these data provide unparalleled clarity in discerning recent divergence, gene flow and demographic history, even among closely related populations or subspecies. The British swallowtail butterfly ( Papilio machaon britannicus ), a habitat specialist restricted to the fenlands of eastern England, is a compelling example of how genomic data can inform subspecies delimitation and conservation status. Through whole‐genome sequencing of P. machaon populations across Europe, we demonstrate that P. m. britannicus forms a genetically distinct and isolated lineage. In contrast, continental subspecies, such as P. m. gorganus and P. m. machaon , are genomically indistinguishable and should be considered a single, widespread subspecies. Although P. m. britannicus displays ~20% lower heterozygosity than its continental relatives, it retains moderate genetic variation and shows no evidence of an elevated load of deleterious mutations. However, we found significantly higher inbreeding and extended runs of homozygosity, which could raise concerns about its long‐term viability. Demographic modelling based on the site frequency spectrum revealed limited power to resolve recent population size changes; however, weak historical gene flow from the continent was inferred. Overall, our study demonstrates the effectiveness of whole‐genome data in resolving fine‐scale population structure and guiding conservation assessments for range‐restricted taxa.

The dynamics of speciation and extinction shape biodiversity over time. The Red Queen hypothesis attributes these dynamics to biotic factors, whereas the Court Jester hypothesis emphasizes abiotic drivers. We investigated how past environmental changes influenced ants (Formicidae) diversification using maximum-likelihood diversification models. We tested whether speciation and/or extinction rates were constant, time-dependent or shaped by variables such as angiosperm and gymnosperm diversities, temperature and sea level fluctuations. We expected biotic factors, particularly angiosperm diversity, to drive ant diversification. Through model selection across 22 diversification scenarios for 30 ant tribes, we found that the environment-dependent models explain nearly half (46%) of diversification patterns, providing comparable support for the Court Jester and Red Queen hypotheses. Angiosperm radiation was not the sole driver of ant diversification, acting as a key factor only for several ant tribes. Instead, temperature and sea level fluctuations often emerged as stronger drivers. These findings suggest abiotic environmental changes played a greater role in shaping ant evolution than previously thought. Comparisons across grafted and non-grafted phylogenies further revealed that taxon sampling can strongly influence diversification analyses. By identifying potential causes of rate variation, this study offers testable hypotheses for understanding the eco-evolutionary processes underlying ant biodiversity.