High-throughput sequencing data, such as target capture, RNA-Seq, genome skimming, and high-depth whole genome sequencing, are used for phylogenomic analyses. Integrating these mixed data types into a single phylogenomic dataset requires several bioinformatic tools and significant computational resources. Here, we present Captus, a novel pipeline to analyze mixed data efficiently. Captus assembles these data types, searches for loci of interest, and produces paralog-filtered alignments. If reference target loci are not available for the studied taxon, Captus can also be used to discover new putative homologs via sequence clustering. Compared to other software, Captus allows the recovery of a greater number of more complete loci across more species. We apply Captus to assemble a comprehensive dataset, comprising the four types of sequencing data for the angiosperm order Cucurbitales, a clade of about 3,100 species in eight mainly tropical plant families, including begonias (Begoniaceae) and gourds (Cucurbitaceae). Our phylogenomic results support the currently accepted circumscription of Cucurbitales except for the position of the holoparasitic Apodanthaceae, which group with Rafflesiaceae in Malpighiales. A subset of mitochondrial gene regions supports the earlier divergence of Apodanthaceae in Cucurbitales. However, the nuclear regions and majority of mitochondrial regions place Apodanthaceae in Malpighiales. Within Cucurbitaceae, we confirm the monophyly of all currently accepted tribes but also reveal hybridization and incomplete lineage sorting both in Cucurbitales and within Cucurbitaceae. We show that contradicting results among earlier phylogenetic studies in Cucurbitales can be reconciled when accounting for gene tree conflict and demonstrate the efficiency of Captus for complex datasets.

Target capture is a common method of generating high throughput DNA sequencing data for phylogenetic reconstruction of species relationships, for which single copy genes are usually most informative. However, a pervasive problem with target capture is that putatively single copy genes may in fact be paralogs resulting from gene duplication, which are problematic for phylogenetic inference because their evolutionary history may differ from the divergence history of species. Here, we use as a case study a target enrichment dataset of 88 species of Detarioideae (Leguminosae) with a focus on the Sindora clade to examine approaches for handling paralogs, including the built-in paralog handling functions in HybPiper and CAPTUS, plus subsequent steps using Putative Paralog Detection and the tree-based Yang & Smith orthology inference approach. We compare the paralogs flagged using these methods and verify their performance with BLAST mapping against a reference genome sequence of Sindora glabra, and then subsequently compare the species tree topologies produced across these methods. Our comparisons of paralogs flagged across the Sindora clade show that the Putative Paralog Detection pipeline was the most accurate in identifying paralogs in terms of its similarity to the BLAST mapping, followed by the built-in paralog identification function of CAPTUS. However, the results we recovered for the Detarioideae subfamily suggest that the largest differences in species tree topology resulted from the use of paralog-filtered alignments (such as with the Putative Paralog Detection pipeline and the Yang & Smith orthology inference approaches) rather than just by removing the sequences of identified paralogous genes. This was the true for HybPiper-assembled datasets but was not seen in CAPTUS-assembled datasets. In all comparisons, the topological differences caused by different paralog handling methods tended to be confined to clades where processes such as hybridisation and introgression are prevalent. Our study provides a roadmap to establish the best approach to identify, eliminate or separate paralogs in the absence of a chromosomally contiguous reference genome for a study group, and highlights the importance of careful data inspection and processing in addition to understanding the extent of paralogy and paralog characteristics (e.g. sequence divergence between copies) for their study group.

Setting conservation priorities for plant genetic resources requires botanical knowledge as well as an assessment of what is under protection to date. In this work we assessed the representation of both plant species richness (SR) and phylogenetic diversity (PD) in the Chilean conservation network, both in-situ and ex-situ. To this end we compiled vascular plant species lists of both Chilean protected wilderness areas (in-situ conservation units) from the literature and from Chilean seed banks, botanical gardens and arboreta (ex-situ conservation units) as a collective effort by their curators. We compiled information for 50 in-situ and 23 ex-situ conservation units (CUs). As a whole, the Chilean conservation network (in-situ + ex-situ CUs) protects 63

Global biodiversity policies recognize the necessity to preserve evolutionary lineages, as their diversity underpins current and future benefits to people and the future of life on Earth. Plants are largely absent from global biodiversity assessments, resulting in a taxonomic imbalance that has undermined their conservation for decades. We present a tree of life and extinction risk estimates for all species of flowering plants (angiosperms), representing a global assessment of their threatened evolutionary history. We estimate that 21.2% of angiosperm evolutionary history is at risk of extinction and identify 9945 priority species that disproportionately account for total threatened evolutionary history. These prioritizations serve to redress imbalances between plants and animals, monitor conservation effectiveness, and optimize resource allocation in the face of increasing human pressures on biodiversity.

Premise: Molecular datasets for estimating phylogenetic trees increasingly include more species and gene regions. Often trees are constructed using backbone phylogenies, subtrees, and other techniques to address the challenges of large dataset size. Currently, there is no established approach to integrate these rapidly expanding datasets. Methods: We generated a phylogenetic tree (and 1,000 bootstrap trees) with divergence times that span euphyllophytes. To do this, we integrated taxonomically broad dated backbone phylogenies with species-level trees generated from phylogenetic analysis of individual clades. Datasets for species-level trees were assembled using PyPHLAWD. Results: The resulting dated phylogenetic tree includes: 121,641 angiosperm species; 1,026 gymnosperms; and 5,603 ferns. This is the largest euphyllophyte phylogenetic tree constructed to date. Topological uncertainty spikes at the start of the Cretaceous and gradually increases during the Cenozoic. Uncertainty in age estimates gradually increases in the Cenozoic but increases dramatically in the most recent 5 Myrs. Discussion: This dated phylogenetic framework can underpin evolutionary studies spanning euphyllophytes, and enable the integration of insights from the recent to the distant past. Our approach also enables the tree to be easily updated in the future to reflect future increases in data availability, and systematic and taxonomic advances within specific clades. ### Competing Interest Statement The authors have declared no competing interest. NSF, DEB 2325835

Obtaining large and well-resolved phylogenetic trees for neotropical clades is challenging, as many species inhabit remote regions, and sampling often relies on herbarium specimens with highly degraded DNA. Target capture provides an effective solution for recovering molecular data from fragmentary material. However, data processing using tools generally designed for diploid organisms and single-copy loci is also challenging, particularly when events such as genome duplication and hybridisation have shaped lineage evolution. We used dual-hybridisation to integrate Ochnaceae-specific and universal probes to reconstruct the phylogenetic relationships of Sauvagesieae, a pantropical clade with ca. 90 species mainly distributed in the northern Andes, the Brazilian Espinhaço Range, and the Amazon-Guyana region. We tested different filtering strategies involving missing data and paralogs to assess probable sources of tree discordance and topological uncertainty. We found no significant benefit in reducing tree discordance after removing entire genes due to the presence of paralogs or a high amount of missing data. Removing fragmentary sequences instead improved alignments and increased branch support of gene trees. By quantifying the proportion of single nucleotide polymorphisms (SNPs), analysing the distribution of the allele frequencies, and gene-tree quartet frequencies, we found signals of polyploidisation and hybridisation, which could reduce resolution at internal nodes, particularly in mountain clades. Our results underscore the importance of exploring the complexities of target-capture data, not only to improve phylogenetic resolution but also to understand the sources of phylogenetic conflict and the underlying molecular evolutionary processes.

The flowering plant genus Erica (Ericaceae) includes well over 800 species and numerous formally described subspecies and varieties. Many of these are threatened in the wild. The Global Conservation Consortium (GCC) for Erica was established under Botanic Gardens Conservation International (BGCI) in order to collaboratively prevent species extinctions. To target this work, we need fundamental information on species distributions, conservation status in the wild, and representation in ex situ collections. In large, complex groups like Erica, such data are not necessarily available or easily accessible. Here, we document the current state of ex situ and in situ conservation of threatened Erica species, identify knowledge and resource gaps, and set out priorities for future work. We further developed and consolidated the large body of data on Erica nomenclature, taxonomy, and diversity now openly accessible as a result of collaborative efforts, in particular through the World Flora Online (WFO), the e-Flora of South Africa, and contributors to the Global Biodiversity Information Facility (GBIF). We obtained accessions data for living plant collections from BGCI’s PlantSearch and from botanic gardens directly, and wild distribution data from GBIF. We linked and summarised data in an updated version (4.03) of the openly available Erica Identification Aid to assist in prioritising work. Through discussions in thematic working groups of GCC Erica we identified further priorities for conservation action. The volume of openly available, georeferenced records for species has increased dramatically in recent years. Although fewer than half of threatened Erica taxa are in ex situ conservation collections, many more botanic gardens hold African/Cape species and could contribute to distributed meta-collections. The most urgent research gaps include undescribed and poorly understood diversity (particularly in South Africa and Madagascar) and shortfalls in up-to-date threat assessments. Between ex situ sites we need to establish accession-level comparisons of data and sharing of conservation grade material. We must improve knowledge of seed longevity and techniques for effective cultivation. We should secure species and collect data through collaboration with landowners and the public. Priority action in situ should include clearance of invasive alien plants as well as habitat restoration and reintroduction. Key statistics for Erica species: 1) Total: 830 species (excluding hybrids; plus 364 subspecies and varieties). South Africa: 747 species; Madagascar/Mascarenes: 41; Tropical Africa: 25; Europe/Mediterranean: 21. 2) 45% species revised taxonomically since 1965. 3) 77% species recorded on GBIF in the last 10 years. 4) 90% species threat assessed (38% in the last 10 years). 5) 46 Critically Endangered (CR), 48 Endangered (EN), 95 Vulnerable (VU) (23% threatened). 6) 47% of threatened species in ex situ collections.

Hybridization and adaptive introgression are increasingly recognized as important components of how natural selection shapes plant speciation and ecological diversification, yet their roles in tropical clades remain poorly understood. We investigated these processes in Pandanus Parkinson (Pandanaceae), a palaeotropical tree genus of high ecological significance and the tenth-most diverse tree genus worldwide. Although morphological evidence suggested hybridization across the Indian Ocean, its genomic basis remained untested. Using 398 total samples (331 nuclear ones for Pandanus), we assessed hybridization and adaptive phenotypes by: (i) testing for broad and morphology-specific transoceanic gene flow through genome-wide conflict, gene conflict, and admixture analyses from Angiosperms353 data; (ii) evaluating whether gene flow occurred via long-distance dispersal or through a bridge clade; and (iii) testing directly and indirectly for adaptive introgression. We found strong, statistically significant evidence of bidirectional transoceanic gene flow, with nuclear clade Ba acting as a critical genetic and biogeographical bridge between Asian and Afro-Malagasy lineages. Contrary to predictions, the striking morphological similarity between geographically disjunct "swamp" lineages reflects convergent evolution rather than shared introgressive history, likely shaped by similarly distinct macroclimatic regimes. Support for adaptive introgression in the bridge clade rested on a consilience of independent evidence: inferred chloroplast capture, differential purifying selection on plastome clades, correlated distribution of a novel foliar water-storage trait, and ecological niche overlap, all coinciding with Miocene forest contraction, Tethys Sea closure, and increasing climatic seasonality. These results highlight hybridization's central role in shaping tropical tree diversity and facilitating ecological adaptation under environmental change.

We investigated here speciation and diversification mechanisms in Turraea and allied genera (Meliaceae-Turraeeae) from Madagascar and continental Africa, as well as their generic delimitations. Our goal was to contribute to an improved understanding of the origin and diversification of the Malagasy and African floras. Using target-enrichment sequencing, we assembled a nuclear dataset comprising 64 taxa (75% of the group's species diversity) to reconstruct phylogenetic relationships within the group. We estimated divergence times and diversification rate shifts and assessed the prevalence of incomplete lineage sorting and introgression/hybridization. The group appears to have originated in the Eocene, probably in southern Africa, with a diversification rate shift occurring in the Miocene coinciding with the colonization of Madagascar. This shift, associated with incomplete lineage sorting and introgression/hybridization, suggests a rapid diversification linked to the onset of the Indian Monsoon. We propose a revised generic classification, including a new key and synoptic descriptions of the genera, to accommodate the polyphyly of Turraea. In this context, we place the endemic Malagasy genera Humbertioturraea and Calodecaryia in synonymy under Turraea, and resurrect the South African genus Nurmonia and the Angolan and Indian genus Naregamia. We therefore publish the necessary new combinations in Nurmonia and Turraea.

Derived woodiness—the evolution of woody growth from herbaceous ancestors—has arisen hundreds of times across flowering plants, yet the environmental conditions associated with its repeated evolution remain poorly understood. Here, we analyse woodiness evolution in the mustard family (Brassicaceae; ~4,150 species) using a time-calibrated phylogeny of 2,927 species, including 374 of the 385 known woody species, together with global growth-form and climatic niche data. We infer 231 independent origins of woodiness alongside 176 reversals to herbaceousness, indicating that woodiness evolves repeatedly but remains evolutionarily unstable. Although woody species are enriched on islands, most occur on the mainland, where woodiness is consistently associated with drought and reduced frost. Correlated-evolution analyses reveal that drought is associated primarily with the persistence of woodiness, whereas reduced frost is associated with gains of woodiness and increased frost with its loss. These findings identify distinct climatic associations with the gain, persistence, and loss of woody growth forms.

A phylogenomic analysis and revised infrageneric classification of Thesium (Santalaceae) is presented based on targeted enrichment using the Angiosperms353 probe set. This first targeted sequencing study includes 137 samples representing 106 species (approximately 32% of the genus). Our results provide substantially improved resolution compared to previous studies that utilised only a few gene regions, with an almost fully supported backbone topology. Thesium (including Austroamericium, Chrysothesium, Kunkeliella, and Thesidium) is confirmed as monophyletic and sister to a clade containing Lacomucinaea and Osyridicarpos. We recognise six monophyletic subgenera with full or strong support: T. subg. Hagnothesium, T. subg. Thesium, T. subg. Spinosa (newly described), T. subg. Discothesium (with revised circumscription), T. subg. Frisea, and T. subg. Psilothesium. We found T. subg. Discothesium as previously delineated to be paraphyletic and describe a new subgenus, T. subg. Spinosa, to ensure monophyly of all subgenera. We formally recognise 18 sections in Thesium, of which 8 are newly described and 2 are raised from lower ranks. Our phylogenetic clades show a strong biogeographic signal and despite sporadic morphological synapomorphies, most subgenera and sections can be distinguished by a combination of their distribution and morphology. We provide the first genetic evidence of potential hybridisation in Thesium paving the way for further exploration of this long-hypothesised compounding factor. This study provides a robust framework for future taxonomic, biogeographic, and evolutionary studies of this diverse and problematic genus.

After publication of our recent article in the Annals of the Missouri Botanical Garden, Volume 111 (published 6 March 2026; Pastore et al., 2026), we discovered that the generic name Chodatia (Paiva) J. F. B. Pastore had already been used for an algal genus, Chodatia Hans­girg (1903). Because algae are governed by the same International Code of Nomenclature for algae, fungi and plants, Chodatia (Paiva) J. F. B. Pastore is therefore a later homonym and illegitimate under Article 53.1 of the Code (Turland et al., 2025). As the name commem­orates the Swiss botanist Robert Hippolyte Chodat (1865–1934), whose work was particularly important in Polygalaceae but also extended to other angiosperms and to phycology, especially green algae, the prior use of the name in algae is perhaps not surprising. We therefore provide the necessary correction and propose Macropolygala J. F. B. Pastore as a replacement name (nomen novum) for Chodatia (Paiva) J. F. B. Pastore. The following nomenclatural changes are therefore required.

Aim Effective implementation of the Global Biodiversity Framework and Global Strategy for Plant Conservation depends on accurate species distribution data. Current vascular plant distribution data, while crucial for understanding terrestrial ecosystems, is often sparse and biased and requires significant expansion. This study developed a scalable approach to prioritize areas for plant occurrence data acquisition, adaptable to national priorities and providing a framework for botanical institutions to coordinate efforts and allocate resources. Location Global. Methods Using a Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) analysis, we prioritized areas based on: (a) ecosystem service value; (b) floristic value threatened by climate or land-use change; and (c) uncertainty in species richness estimates, stratified by biome and region. Regional prioritization maps for Africa & Madagascar; East, South and Southeast Asia; Siberia and the Russian Far East; South America; and North & Central America were reviewed by botanical experts for validation. Scalability was assessed by comparing regional and global analyses. Results Data-driven priority maps, divided into tree-dominated and grassland/deforested areas, largely received expert support. High similarity between global and regional maps demonstrated scalability. Main conclusions Our approach provides a framework for supporting national implementation of the Global Biodiversity Framework. Variables and their weights can be tailored to national or local needs. The method’s flexibility and adaptability extend to other taxonomic groups and objectives, such as protected area selection. By prioritizing data acquisition, whether field-based or digital, this research promotes the efficient use of resources. A key advantage of this approach is its capacity to systematically translate expert opinion into explicit and quantitative criteria, which in turn facilitates clear communication with policymakers and funders. ### Competing Interest Statement The authors have declared no competing interest. 3T's Foundation, UK

BACKGROUND AND AIMS:Macroevolutionary studies of species-rich plant lineages have often focused on processes behind either their large distribution or their morphological and functional diversity. Integrating these two evolutionary mechanisms is essential to capture the full picture of how evolutionary and ecological processes shape the biogeographical history of major plant lineages. We investigate whether reproductive and vegetative traits are associated across the evolutionary history of Thymelaeaceae and whether they facilitated dispersal and establishment of lineages across continents and ecological niches. METHODS:We use an integrative framework combining: (1) phylogenomics with the Angiosperms353 probe set; (2) detailed characterisation of vegetative architectures and diaspore traits; (3) extraction of species distribution and pedoclimatic data from global databases; (4) multivariate analyses to assess trait-environment associations; (5) correlated evolution tests; (6) ancestral state reconstructions of four vegetative and reproductive traits; and (7) inferences of ancestral ranges and ecological niches, explicitly accounting for dispersal effects. KEY RESULTS:Architectural models and fruit types were significantly associated with canopy openness, with basitonic architectures associated with open habitats. The biogeographical reconstructions suggest an evolutionary history shaped by both vicariance and long-distance dispersal. Red, fleshy fruits evolved repeatedly but played little role in intercontinental dispersal; they instead support a c. 13-fold increase in the probability of transition between pedoclimatic niches. Additionally, major biome shifts consistently coincided with changes in architectural models. CONCLUSIONS:Throughout the evolutionary history of Thymelaeaceae, our study demonstrates that large plant lineages occupying various vegetation types worldwide possess reproductive and vegetative strategies influenced by different ecological drivers, with reproductive traits primarily shaped by dispersal agents and vegetative traits by abiotic environmental factors. Our study provides evolutionary scenarios supporting the coordinated, but not correlated, evolution of reproductive and vegetative adaptations that enable lineages to diversify into different habitats and partly circumvent phylogenetic niche conservatism.

Abstract The plant family Plantaginaceae comprises approximately 2100 species in 106 genera, representing around 1% of all eudicots. The current circumscription of the family has been established in recent decades based on insights from DNA‐based phylogenetic analyses, which have united genera previously considered unrelated. Consequently, the family exhibits a worldwide distribution and immense diversity in habitats and morphological traits, ranging from aquatic herbs in tropical regions, through alpine genera in the Himalayas, to carnivorous plants on low‐nutrient sandy soils. Here, we present the first phylogenomic analysis and the most comprehensive study on Plantaginaceae systematics to date in terms of taxon coverage, addressing several uncertainties and providing new insights into relationships within and among tribes. This is achieved through high‐throughput sequencing in combination with the Angiosperms353 probe kit. A concatenated and a coalescent tree were built, based on an alignment of 132 individuals, representing 92–99 genera. All 12 tribes were recovered as monophyletic. Notably, we found that genera Ildefonsia and Uroskinnera are not members of the family, and we evaluated the relationships of Cheilophyllum and Kashmiria for the first time. The results are discussed in the form of a tribe‐based review, offering an overview of the classification history of the tribe, past and current placements of genera and outstanding questions that remain to be solved.

Biome conservatism is prevalent during the evolution of plant lineages. However, studies assessing biome lability, i.e. the capacity to shift biomes and its impact on tropical tree species diversification is currently limited. To address this, we analysed an endemic lineage of African tropical trees to investigate phylogenetic patterns of biome conservatism and lability and their impact on speciation and extinction rates. We reconstructed a time-calibrated phylogeny of the Berlinia clade (16 genera, 201 species) using 140 nuclear genes, 75% of its extant species and two fossil calibrations. We found the forest biome as the ancestral habitat and we inferred nine independent shifts from forest to savanna with no reversals. The forest biome is mostly conserved within the Berlinia clade, while the ability to shift to the savanna biome is randomly distributed across the group. We found five palaeoendemic genera that have persisted solely in the forest biome since the Oligocene. However, the ability to shift among biomes does not seem to influence speciation or extinction rates. Our results suggest that palaeoendemic and forest-restricted lineages are more susceptible to habitat alterations and climate change than lineages with biome lability, due perhaps to an innate limitation to adapt to new habitat types.

Tropical rainforests are home to almost half of plant diversity, yet a shortfall in phylogenetic hypotheses for tropical plants hinders our understanding of how rainforests have formed and adapted to past global changes. Phylogenetic and historical biogeographic evidence from key rainforest lineages, such as palms (Arecaceae), are required to illuminate the history of these ecosystems. However, our current understanding of the palm tree of life is based on uneven sampling of plastid and nuclear data. Moreover, numerous palm genera and palm fossils have been described or revised over the past decade, casting doubt on palm relationships, ages and ancestral ranges inferred in early studies. Here, we infer the phylogenetic relationships of all 184 palm genera based on data from 1,033 nuclear genes generated using target sequence capture. Our palm phylogenomic tree is highly resolved and supported. Remaining areas of ambiguity reflect the complex dynamics of palm evolution, including rapid diversification events in subfamily Arecoideae and putative cases of ancient reticulation throughout the family. We undertake a comprehensive review of the palm fossil record and use a vetted selection of fossils to estimate divergence times with two Bayesian methods, the first based on calibration of five nodes using the age of fossils assigned to them, and the second based on co-estimation of divergence times and phylogenetic placements of 113 fossils with a Fossilized Birth-Death model. We then use the distribution ranges of extant and fossil taxa to infer ancestral ranges. We show that the palm family first diversified in the Early Cretaceous in regions corresponding to what is now North, Central and South America and Oceania, that many tribes and subtribes had originated by the Late Cretaceous, and that two thirds of the genera had diverged by the Oligocene. Fossil-informed analyses provide a more complex picture of the early biogeography of palms than analyses relying only on the ranges of extant taxa. Despite uncertainties regarding fossil placement, it is clear that palms dispersed dozens of times across oceanic gaps, and that dispersal and extirpation patterns are consistent with an ancient affinity of palms for megathermal climates. Our dated phylogenomic trees and curated fossil dataset provide a new foundation for evolutionary studies on palms, opening the door to deeper research on the rainforest biome in which they thrive.

Phylogenetic classification based on evolutionary relationships is the standard approach in systematics, but Cactaceae has posed significant challenges due to the signature of its rapid radiation: low sequence divergence hindering phylogenetic resolution and enormous species diversity hindering attempts to adequately reflect phylogenetic diversity. Previous classifications mostly relied on joint assessment of multiple phylogenetic studies and/or intuition on morphological evolution, lacking comprehensive genomic analysis. Here, we propose a revised phylogenetic classification of Cactaceae, based on the Angiosperms353 set of phylogenomic markers, including 170 species, covering close to 90

Extinction results in not only loss of species, but also loss of the unique evolutionary history that they represent and the irreplaceable features they exhibit. There is broad consensus regarding the necessity to optimise the preservation of the tree of life by including evolutionary information in conservation prioritisation, a notion also endorsed by major policy frameworks[1][1]–[4][2]. However, evolutionarily-informed prioritisations are lacking for most plants, resulting in a taxonomic imbalance in the evolutionary information incorporated in global biodiversity analyses, which has undermined conservation for decades. Here, we use comprehensive species-level phylogenetic trees, and extinction risk estimates, to generate the first global assessment of angiosperm evolutionary history at risk, and to identify phylogenetically-informed conservation priorities for the world’s flowering plants. We estimate that more than one fifth of angiosperm evolutionary history is at risk of extinction in the short term. Using the Evolutionarily Distinct and Globally Endangered[5][3],[6][4] approach, we identify 9,945 threatened plant species that disproportionately account for total evolutionary history at risk. Species and area prioritisations incorporating evolutionary history are urgently needed to correct imbalances between plants and animals, monitor the effectiveness of conservation efforts, and optimise conservation resource allocation in the face of increasing human pressures on Earth’s biodiversity. ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1 [2]: #ref-4 [3]: #ref-5 [4]: #ref-6