Sidonie Bellot

Bulbostylis is the second‐most species‐rich genus in Abildgaardieae, comprising c. 221 species with a pantropical to warm‐temperate distribution and a remarkable ecological and morphological diversity. Despite advances in molecular phylogenetics confirming its monophyly, relationships within Bulbostylis remain poorly resolved, and previous attempts at creating infrageneric classifications are either geographically restricted or unsupported by phylogenetic evidence. Previous molecular studies have sampled fewer than 20% of the species of the genus, limiting our understanding of its evolutionary history. Here, we investigate relationships among 149 species and 3 subspecies of Bulbostylis , representing 69% of global diversity, using a universal probe kit for targeted genomic sequencing of flowering plants (Angiosperms353 probe kit). Our sampling also includes the genus Nelmesia , which we found to fall within Bulbostylis . We propose a new infrageneric classification and suggest a set of diagnostic morphological characters. Our revised infrageneric classification for Bulbostylis includes 18 sections and 8 subsections, providing a foundation for future taxonomic and evolutionary studies of this ecologically important genus.

Species delimitation based only on morphological characters can be challenging in groups where morphology is highly variable or difficult to study. In such cases, molecular data may be used to test the robustness of morphology-based taxonomic treatments. In Cyperaceae, phylogenomic studies have helped clarify relationships and taxon delimitation at the genus level and above, but species delimitations and relationships remain poorly documented in many genera, notably Bulbostylis (hairsedges). Bulbostylis is a morphologically diverse and taxonomically complex group, with Madagascar representing one of its centres of endemism. Species delimitation within the genus has long been hindered by the scarcity of stable diagnostic characters and the absence of molecular data. To evaluate whether the Malagasy Bulbostylis species correspond to distinct evolutionary lineages, we sequenced 353 nuclear loci (Angiosperms353) from 102 specimens collected between 1805 and 2023, including herbarium and silica-dried material. After removing samples with low sequencing success, 64 accessions representing 25 species were retained. Target sequence capture data were analysed using standard phylogenomic approaches, including sequence alignment, maximum likelihood gene tree inference, and species tree inferences using maximum likelihood and multispecies coalescent summary approaches. Phylogenetic analyses recovered 13 well-supported clades corresponding to taxa currently recognised based on morphological characters ( B. andringitrensis , B. barbata , B. erectopallescens , B. festucoides subsp. bathiei , B. filamentosa , B. firingalavensis , B. hispidula , B. mahafalensis , B. micranthera , B. renschii , B. schoenoides , B. tristicha , B. viguieri ), and highlighted a possible case of budding speciation with B. trichobasis being nested inside B. andringitrensis in the species trees. Potentially undescribed taxa closely related to B. flaccidula and B. pseudocollina were identified, while another ten species will require further investigation due to low or no data availability. Additional field collection of fresh material, together with sequencing and analysis of other herbarium specimens, will be necessary to fully understand species delimitations in these lineages. These results indirectly show that morphological characters such as inflorescence architecture, glume morphology, leaf sheath, and nutlet features remain highly reliable for species identification in Malagasy Bulbostylis .

Speciation shapes biodiversity, yet why some lineages diversify faster than others remains unclear. Theory predicts that traits promote ecological speciation through adaptation, but their evolvability (‘trait flexibility’) may be impacted by allometric and genomic constraints. Here we test this by integrating phylogenetic, trait and genome size data for palms (Arecaceae)—a large pantropical family (>2500 species) with 167-fold variation in certain traits (e.g. fruit size) and 60-fold genome size variation. Using structural equation modelling, we test three hypotheses: trait evolution promotes speciation (H1: trait flexibility hypothesis), and speciation and trait evolution rates are constrained by allometry (H2: allometric constraint hypothesis) and genome size (H3: large genome constraint hypothesis). We detected seven major speciation rate shifts during approximately 110-million-years of palm evolution. Tip-derived speciation rates increased with faster evolution in leaf size and plant height, supporting H1, whereas correlated evolution between all traits indirectly influenced speciation, supporting H2. Large genomes were associated with decreased plant height and stem diameter evolution rates supporting H3, but the genome size-speciation association was sensitive to phylogenetic autocorrelation. Our findings illustrate how the interplay between genome size, allometry and trait evolvability affect speciation, emphasizing the importance of holistic approaches for uncovering general mechanisms driving speciation throughout the Tree of Life.

Premise: DNA barcoding for timber species identification requires comprehensive reference datasets, informative DNA barcodes, and cost‐effective protocols. We developed a workflow leveraging Hyb‐Seq (target capture sequencing and genome skimming) to address these challenges, and we tested it on four genera from the mahogany family (Meliaceae). Methods: We sequenced up to 350 nuclear and 177 plastid loci from 132 herbarium specimens representing leaf samples of 22 species. We determined the DNA barcoding potential of each locus by looking at species recovery and monophyly in gene trees. We then selected 13 short regions (candidate barcodes) within high‐potential loci and tested their PCR amplification and Sanger sequencing on wood DNA. Results: Three candidate barcodes emerged as the most reliably sequenced from wood DNA and as providing the most accurate species‐level identifications, with species monophyly rates above 80%. Failure to obtain sequences from some wood DNA extracts was more often associated with potential DNA impurity (as inferred from DNA color) than with DNA degradation. Discussion: Our reference data and candidate barcodes provide a foundation to support the DNA barcoding of mahogany and its relatives. Our workflow illustrates how the wealth of Hyb‐Seq data currently generated from global herbaria may be leveraged to monitor plant diversity.

Summary: The importance of functional trait evolution and genome size on plant speciation are well established, but their interactive effects remain untested in a single comparative macroevolutionary framework. We integrated phylogenetic, trait and genome size data for palms (Arecaceae) – a large pantropical family (>2600 species) with 167-fold variation in trait and 60-fold variation in genome size. We used structural equation modelling to test three key hypotheses: trait evolution promotes speciation (H1: trait flexibility hypothesis), and, speciation and trait evolution rates are constrained by allometry (H2: allometric constraint hypothesis) and genome size (H3: large genome constraint hypothesis). We detected seven major speciation rate shifts during the ca. 110-million-year history of palms. Tip-derived speciation rates increased with faster evolution in leaves and plant height, supporting H1, whereas correlated evolution between trait evolution rates indirectly influenced speciation, supporting H2. Large genomes decreased plant height and stem diameter evolutionary rates, but increased leaf size evolution and speciation rates, thus partly supporting H3. Our findings illustrate how the complex interplay between genome size, allometry and trait evolvability affect speciation, emphasizing the importance of holistic approaches in macroevolution. Furthermore, our results point to potential general mechanisms driving speciation rates throughout the plant Tree of Life.

With ca. 200 morphologically variable species placed in 20 putative genera within the tribe Selineae of subfamily Apioideae, the Perennial Endemic North American (PENA) clade of Apiaceae forms the second‐largest plant radiation entirely endemic to North America, yet, elucidating evolutionary relationships for this intractable plant lineage has been challenging. The objectives of this study are to elucidate the monophyly of the PENA clade and assess phylogenetic relationships to other clades in Selineae, contributing to a refined understanding of relationships. By analyzing a robust sample set, including ingroup and outgroup taxa, we employ high‐throughput sequencing technologies to capture a wide array of nuclear DNA sequences using the Angiosperms353 baits. Our bioinformatics pipeline, incorporating both HybPiper and HybPhaser workflows, facilitated the recovery and analysis of targeted sequences, ensuring high‐quality data for maximum likelihood and multispecies pseudo‐coalescent phylogenetic reconstructions. Our phylogenetic analyses do not recover a monophyletic PENA that includes all genera presumed to be part of this clade. Our results prompted the realignment of genera to include in the PENA clade. Genera that occur primarily in eastern North America are moved out of PENA. We also resolve, for the first time, the placement of the genus Eurytaenia within Apiaceae. This study contributes to a deeper understanding of the phylogenetic relationships within a taxonomically complex group of western North American Apiaceae, paving the way for broader insights into plant diversity and evolution in this botanically complex region.

The palm family (Arecaceae) has a rich history of phylogenetic research, including several recent phylogenomic studies. However, densely sampled phylogenomic datasets for larger palm clades – such as subfamilies – are still few in number. We used target sequence capture to obtain data for 971 nuclear genes across 421 (ca. 80%) species in the subfamily Coryphoideae. We inferred a robust phylogenetic tree to address systematic issues in the subfamily, specifically the relationships among tribes Cryosophileae, Sabaleae, Phoeniceae and Trachycarpeae, the affinities of seven genera in Trachycarpeae that are not currently assigned to any subtribe, and the monophyly of genera across the subfamily. We recovered relationships among tribes that are in accordance with other major nuclear phylogenomic datasets, but that are incongruent with trees derived from plastome sequences. Importantly, the placement of tribe Phoeniceae (the date palms) remains contentious. Our tree recovered with high support the relationship of all unplaced Trachycarpeae genera, paving the way for an updated classification. Most genera were resolved as monophyletic except for Livistona and all three genera of tribe Caryoteae, calling for a revision of generic limits. Our tree clarifies the relationships of many fan palm species for the first time, allowing for future studies of diversification, trait evolution or biogeography.

Understanding the impact of climate change on the functional trait composition (and hence ecosystem functioning) of tropical alpine regions is critical for predicting biodiversity responses. We tested the effects of a decade of warming on the morphological, chemical and genomic traits of Páramo species using open-top chambers (OTCs). We conducted vegetation surveys and collected samples from individuals inside and outside the OTC plots to estimate differences between treatments (warming versus control). Vegetation cover decreased over time in both treatments suggesting a potential decline in soil moisture in our study area. Warming led to a reorganization of the trait space and trait network structure. Species showed a wide range of responses to warming, with significant changes across different trait combinations. Nevertheless, we did not find significant differences in trait values or the direction of change between species whose percentage vegetation cover increased in OTC (or decreased less) over time, compared with control. Community-weighted mean values of plant height, leaf area, leaf dry matter content, genome size, leaf C and P, significantly increased over time only in OTC plots (i.e. traits associated with carbon storage and decomposition). While warming and reduced soil moisture lead to heterogeneous species responses without a clear winning trait strategy, changes at the community level may have important implications for Páramo ecosystem functioning.

Distributed across two continents and thousands of islands, the Asian tropics are among the most species-rich areas on Earth. The origins of this diversity, however, remain poorly understood. Here, we reveal and classify contributions of individual tropical Asian regions to their overall diversity by leveraging species-level phylogenomic data and new fossils from the most species-rich Asian palm lineage, the rattans and relatives (Arecaceae, Calamoideae). Radiators (Borneo) generate and distribute diversity, incubators (Indochina, New Guinea, and Sulawesi) produce diversity in isolation, corridors (Java, Maluku, Sumatra, and the Thai-Malay Peninsula) connect neighboring regions, and accumulators (Australia, India, Palawan, and the Philippines) acquire diversity generated elsewhere. These contrasting contributions can be explained by differences in region size and isolation, elucidating how the unique island-dominated geography of the Asian tropics drives their outstanding biodiversity.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods^1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome^3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins^5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹ provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.