William John Baker

Premise: Molecular datasets for estimating phylogenetic trees increasingly include more species and gene regions, and trees are often 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 1000 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, 1026 gymnosperms, and 5603 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 Myr. 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 increases in data availability, as well as systematic and taxonomic advances within specific clades.

Premise: Although the megafossil flora of the upper Albian–lower Cenomanian Dakota Formation in Kansas is well known for angiosperms, monocots have not been reported previously. Methods: A mesofossil flower was discovered by X‐ray analysis of a specimen collected more than a century ago from the Dakota Sandstone of central Kansas. A mid‐Cretaceous (ca. 100 Ma) age is inferred from its stratigraphic provenance close to the Albian–Cenomanian boundary. Successive virtual transverse and longitudinal sections and a three‐dimensional rendering generated from micro‐CT scanning facilitate recognition of the floral parts and their organization. Results: The flower is about 1.5 mm high and 1.2 mm in diameter, is actinomorphic and borne on a slender pedicel, and possesses three free sepals alternating with three free, coriaceous petals and six stamens in two whorls, one opposite the petals, and the other opposite the sepals. The gynoecium consists of three apocarpous, flask‐shaped carpels, each with a ventral apical stigmatic groove. Conclusions: This flower, which we name Tomlinsoniella pedicellata gen. et sp. nov., constitutes the first mesofossil evidence for monocots in the Dakota Formation. Importantly, it also appears to be the earliest unequivocal fossil evidence for the appearance of the trimerous‐pentacyclic floral plan typical of many monocots. Among extant monocots, this combination of characters is most consistent with the coryphoid palm lineage, although the fossil could also belong to an extinct monocot clade. If correct, this represents the earliest known mesofossil record of a commelinid monocot.

The Urticaceae (∼2600 species) were first formally recognized by Jussieu in the 18th century and last comprehensively monographed by Weddell in the 19th century. Since Weddell’s work, family delimitation has been modified and many genera described in a fragmented manner. Over the past two decades, numerous molecular studies have supported the inclusion of Cecropiaceae within Urticaceae and identified paraphyly in several genera, notably Laportea, Urera, Boehmeria, Parietaria, Pellionia, and Pouzolzia. This study aimed to provide a robust, updated classification for Urticaceae by (i) increasing taxon and genomic locus sampling through the integration of newly generated sequence data with previously published datasets; and (ii) incorporating morphological data to support a revised delimitation of tribes and genera, and to establish a new linear sequence for the family. We also sought to identify remaining taxonomic challenges. Using Sanger and Angiosperms353 sequence data, we constructed a phylogenetic framework for 57 out of 59 currently accepted genera. We also assessed the phylogenetic informativeness of 57 morphological characters by mapping them onto the phylogeny. Our analyses support the delimitation of 54 monophyletic genera and an infrafamilial classification comprising seven tribes, one of which we describe as new: Myriocarpeae. We provide a revised linear sequence for the family. Our classification reinstates several names previously treated as synonyms (Fleurya, Leptocnide, Margarocarpus, Polychroa, Scepocarpus, Sceptrocnide), places several genera in synonymy (Hemistylus and Rousselia under Pouzolzia; Hesperocnide under Urtica; Gesnouinia and Soleirolia under Parietaria), and proposes the recognition of two new genera, Muimar gen. nov. and Pouzolziella gen. nov., to accommodate Boehmeria nivea and Pouzolzia australis, respectively. Mapping morphological characters onto the phylogeny indicates that while most states are homoplastic at the family level, their combination is valuable for recognizing genera. Geographic character mapping suggests a high degree of spatial conservatism at the genus rank. Our dated ultrametric tree suggests an origin for Urticaceae in Indomalaya during the mid-Cretaceous, followed by establishment in the Laurasian boreotropical flora and subsequent dispersal to the Neotropics and Africa. Once classified within an evolutionary framework we believe that the Urticaceae represent a valuable study system in evolutionary biology for investigating transitions across biomes, the drivers of trait evolution, and intrinsic speciation mechanisms. New tribe: Myriocarpeae New genera: Muimar, Pouzolziella

Tropical Asia hosts an exceptionally diverse and unique biota, but comprehensive estimates of species diversity and endemism are unavailable for its many subregions, and gaps in biodiversity knowledge and conservation assessments remain unexplored. Here, we synthesize biodiversity data from tropical Asia to assess patterns of species richness, endemism, data completeness, species discovery, and extinction risk across major plant and animal groups. We show that the Asian tropics harbour nearly one quarter of the known global diversity among taxa examined on average while being much smaller in extent than other tropical realms, probably due to its insular and archipelagic geography. Rates of species discovery remain high for many terrestrial and freshwater groups especially in Indochina, South Asia and Borneo, indicating substantial undocumented diversity. Considerable spatiotemporal shortfalls in species occurrence data exist, particularly across Indonesia. Among assessed species, about one-third of vascular plants, one fifth of the land and freshwater vertebrate fauna, one-third of reef-building corals, and almost half of the region’s shark and ray species are threatened with extinction. However, conservation assessments are lacking for many invertebrate species, and almost one-sixth of assessments are over a decade old and thus may not be keeping pace with intensifying human pressures across the region. Our analysis highlights the critical need for increased investment and effort to better document, monitor, study, and safeguard tropical Asia’s rich natural heritage.

We present here a revision of the APG classification that considers the extensive recent analyses of hundreds of nuclear and plastid genes for many angiosperm species. Although previous versions of the APG classification were largely based on uniparentally inherited markers (plastid DNA, typically maternally inherited), there has emerged since APG IV extensive evidence of widespread hybridization and inheritance of ancestral polymorphisms. Despite this evidence of gene‐tree discordance, most of the APG IV classification is supported by both plastid and nuclear analyses, and only a few revisions are required in this update to make the classification parallel phylogenetic results in the literature. At the ordinal level, few changes in circumscription are required relative to the last APG version, although the fabids now comprise only the four nitrogen‐fixing orders (Cucurbitales, Fabales, Fagales, and Rosales) and the malvids now include the former COM clade (Celastrales, Malpighiales, and Oxalidales), which, in nuclear DNA analyses, is no longer monophyletic. Oncothecales (with only Oncothecaceae) and Cardiopteridales (with Cardiopteridaceae and Stemonuraceae) are newly recognized, and Icacinales are restricted to Icacinaceae. Restriction of Aquifoliales and Bruniales to just Aquifoliaceae/Helwingiaceae and Bruniaceae, respectively, is also proposed. Huaceae and Columelliaceae are unplaced to order among the malvids and campanulids, respectively. At the family level, expanded circumscriptions include Tecophilaeaceae (including Ixioliriaceae, Asparagales), Frankeniaceae (including Tamaricaceae, Caryophyllales), Phytolaccaceae (including Agdestidaceae and Sarcobataceae, Caryophyllales), Helwingiaceae (including Phyllonomaceae, Aquifoliales), Gesneriaceae (including Calceolariaceae and Peltantheraceae, Lamiales), Pentaphylacaceae (including Sladeniaceae, Ericales), and Orobanchaceae (including Mazaceae, Paulowniaceae, Phrymaceae, and Wightiaceae, Lamiales). In Santalales, the limits of Santalaceae and Olacaceae are revised, and Erythropalaceae and Strombosiaceae are recognized as distinct from Olacaceae; Balanophoraceae are maintained as distinct from Santalaceae, but this is a tentative placement. Generic relationships in Dioscoreales require more analyses before a revised family classification can be proposed, so we maintain the APG IV families of this order.

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.

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.

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 characterization 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 an ∼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 shaped primarily 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.

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 data set 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 data set, comprising the four types of sequencing data for the angiosperm order Cucurbitales, a clade of about 3100 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 data sets.