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Angiosperm Phylogeny Group

The Angiosperm Phylogeny Group (APG) is an informal international collaboration of systematic botanists dedicated to developing a consensus-based classification of flowering plants (angiosperms) grounded in phylogenetic evidence from molecular and morphological data.^[1] Established to address inconsistencies in traditional taxonomy, the APG emphasizes monophyletic groups—clades that reflect evolutionary relationships—rather than artificial groupings based on shared traits alone.^[2] This approach has revolutionized angiosperm systematics by integrating cladistic principles, making it a cornerstone for modern botanical research and herbaria organization. The APG's work began with its inaugural publication in 1998, which proposed an ordinal classification for 462 angiosperm families organized into 40 orders and several informal higher-level clades, such as monocots, eudicots, rosids, and asterids.^[2] This was followed by refinements in subsequent updates: APG II (2003) expanded options for family circumscriptions to accommodate emerging data while maintaining stability; APG III (2009) consolidated families, reducing the total to 413 and orders to 59 by prioritizing stricter monophyly; and APG IV (2016) further updated the system to include 416 families across 64 orders, incorporating new phylogenetic insights and recognizing additional orders like Boraginales and Dilleniales, which remains the latest update as of 2025.^[1] These iterations reflect ongoing advancements in DNA sequencing and global collaboration among experts, ensuring the classification evolves with scientific evidence.^[1] Key contributors to the APG include prominent botanists such as Mark W. Chase, Peter F. Stevens, and Kåre Bremer, who have coordinated efforts across institutions like the Royal Botanic Gardens, Kew, and the Missouri Botanical Garden.^[2]^[1] The system's influence extends beyond academia, informing conservation priorities, ecological studies, and practical applications in agriculture and horticulture by providing a stable, evidence-based framework for identifying evolutionary lineages among the approximately 350,000 angiosperm species.^[3]

Overview

Definition and Purpose

The Angiosperm Phylogeny Group (APG) is an informal international collaboration of systematic botanists dedicated to developing a consensus-based classification of flowering plants (angiosperms). Founded in the 1990s, the group emerged from discussions among researchers seeking to reconcile emerging phylogenetic insights with traditional taxonomy.^[4]^[5] The primary purpose of the APG is to establish a stable, phylogeny-driven system that prioritizes monophyletic groups—clades sharing a common ancestor—over the artificial categories prevalent in earlier Linnaean hierarchies. This approach aims to reflect evolutionary relationships more accurately, serving as a reference framework for botanists, ecologists, and other scientists studying plant diversity. By superseding outdated classifications, the APG system facilitates clearer communication about angiosperm evolution and supports ongoing taxonomic research.^[4]^[2] The initiative was motivated by the rapid influx of DNA sequence data in the late 1980s and early 1990s, which, combined with morphological evidence, highlighted discrepancies in conventional systems like those of Cronquist (1981) and Takhtajan (1997). These molecular datasets, including genes such as rbcL and 18S rDNA, enabled cladistic analyses that revealed new phylogenetic structures, necessitating an updated classification to integrate both molecular and morphological data for a more robust understanding of angiosperm relationships.^[4]^[5]

Historical Context in Angiosperm Taxonomy

Prior to the advent of molecular data, angiosperm classification systems were predominantly based on morphological and anatomical traits, such as flower structure, inflorescence patterns, and vegetative features. Arthur Cronquist's 1981 system represented a major synthesis of these approaches, organizing flowering plants into two classes—Magnoliopsida (dicotyledons) and Liliopsida (monocotyledons)—subdivided into 11 subclasses, 64 orders, and numerous families, with an emphasis on evolutionary trends like increasing specialization in pollination and seed dispersal mechanisms. However, this and similar pre-molecular frameworks, including those by Takhtajan (1980) and Thorne (1983), frequently resulted in paraphyletic or polyphyletic groupings that did not accurately reflect shared ancestry, as groups were often assembled for convenience based on superficial similarities rather than strict monophyly. For instance, the dicotyledons as a whole were later recognized as paraphyletic due to the nested position of monocotyledons within them, underscoring inherent limitations in morphology-driven taxonomy.^[6] The 1980s marked the rise of cladistics in plant systematics, a method pioneered by Willi Hennig that prioritizes monophyletic clades defined by synapomorphies (shared derived characters), challenging the evolutionary but non-cladistic arrangements of earlier systems. This shift was propelled by computational advances enabling parsimony-based analyses of morphological data, as seen in early cladistic studies of land plants that questioned traditional hierarchies. Simultaneously, molecular phylogenetics emerged as a transformative tool, with initial DNA sequencing efforts in the late 1980s providing objective character data less prone to convergence or homoplasy seen in morphology. These developments exposed significant conflicts in traditional classifications; for example, the subclass Hamamelidae—traditionally united by traits like wind pollination and reduced perianth—was revealed through cladistic and early molecular analyses to comprise disparate lineages scattered across the angiosperm tree, rendering it polyphyletic and highlighting the inadequacy of morphological groupings for capturing deep evolutionary relationships.^[7]^[8] Key milestones in this transition included pioneering molecular studies using the chloroplast-encoded rbcL gene, which encodes the large subunit of Rubisco and offered a slowly evolving marker suitable for higher-level phylogeny. The first rbcL sequences for angiosperms appeared in the mid-1980s, but landmark phylogenetic analyses in the early 1990s, such as Chase et al.'s 1993 study of over 500 taxa, demonstrated a rapid early diversification of angiosperms and resolved major clades like eudicots and core angiosperms with strong support. Subsequent molecular clock calibrations, integrating rbcL with other loci like 18S rDNA and atpB, estimated the crown-group age of angiosperms at approximately 140–180 million years ago in the Middle Jurassic to Early Cretaceous, aligning with but refining fossil evidence and emphasizing the explosive radiation that traditional systems had underestimated.^[9]^[10]

Principles and Methodology

Core Principles

The Angiosperm Phylogeny Group (APG) establishes its classifications on a foundation of phylogenetic principles designed to reflect evolutionary relationships accurately while ensuring usability in botanical practice. Central to this approach is the commitment to monophyly, requiring that all recognized taxa—such as orders and families—constitute clades, encompassing a common ancestor and all its descendants. This principle rejects paraphyletic assemblages, such as the traditional subclass Magnoliopsida (dicotyledons), which exclude certain lineages like monocots despite shared ancestry, thereby promoting a natural hierarchy based on shared evolutionary history. Complementing monophyly is the APG's consensus-driven methodology, which synthesizes evidence from multiple molecular phylogenetic studies rather than relying on isolated research. Classifications emerge from collaborative agreement among systematists, incorporating data from genes like rbcL, atpB, and 18S rDNA to identify robust clades, while treating placements with weak support as optional to accommodate ongoing uncertainties. This iterative process, refined through expert input and periodic updates, prioritizes stability and broad acceptance over rigid adherence to preliminary findings.^[1] Practicality remains a guiding tenet, balancing scientific rigor with the needs of users such as educators, conservationists, and horticulturists. The APG retains familiar names and structures where phylogenetically justified, employs taxonomic ranks flexibly to avoid unnecessary fragmentation, and circumscribes larger families to minimize proliferation without compelling evidence. For instance, monofamilial orders are limited to cases of strong support, ensuring the system remains accessible and stable for global application.^[1]

Data Sources and Analytical Methods

The Angiosperm Phylogeny Group (APG) classifications are constructed primarily from molecular phylogenetic data, drawing on multi-gene sequences to capture evolutionary relationships across angiosperm diversity. Key data sources include plastid genes such as rbcL, matK, atpB, and ndhF; nuclear ribosomal genes like 18S rDNA; and, in later iterations, mitochondrial genes and low-copy nuclear loci. These are supplemented by morphological, anatomical, and other non-molecular characters where molecular data are limited, ensuring comprehensive evidence for clade support. Sampling emphasizes broad representation, encompassing over 300 families and thousands of genera to reflect angiosperm-wide patterns, with datasets often including 640 or more taxa in multi-gene analyses.^[2]^[11] Analytical methods center on cladistic approaches, including parsimony-based tree searches to infer most parsimonious phylogenies from aligned sequence data, often using software like PAUP* for heuristic searches with tree-bisection-reconnection branch swapping. Maximum likelihood (ML) methods, implemented via programs such as PHYML or RAxML, model nucleotide substitution processes (e.g., GTR + Γ + I) to estimate likelihoods and construct optimal trees. Clade robustness is assessed through non-parametric bootstrapping or jackknifing, with support thresholds typically set at 50–70% for inclusion in the consensus classification; higher values (>95%) indicate strong evidence for monophyly. Fossil-calibrated molecular clocks, using tools like BEAST or r8s, integrate paleontological data to estimate divergence times, aiding in the temporal context of clades.^[2]^[12] The evolution of APG methods reflects advances in phylogenomics, shifting from single-gene analyses in early versions—primarily rbcL and 18S rDNA under parsimony—to multi-locus datasets in subsequent updates, incorporating up to 17 genes across nuclear, plastid, and mitochondrial genomes for improved resolution. Bayesian inference, via MrBayes or similar, emerged in APG II and became prominent by APG IV, allowing probabilistic modeling of uncertainty through Markov chain Monte Carlo sampling and posterior probability assessments for clades (often requiring >0.95 support). This progression enhances accuracy by addressing issues like long-branch attraction and incomplete lineage sorting, while maintaining emphasis on monophyly through rigorous support validation; ongoing work towards APG V (presented 2024) further emphasizes phylogenomics using nuclear loci and genome assemblies to resolve gene tree conflicts.^[11]^[13]^[14]

Evolution of the APG System

APG I (1998)

The Angiosperm Phylogeny Group (APG) published its inaugural classification system in 1998, marking a significant shift toward a molecularly informed, cladistic framework for angiosperm taxonomy. Titled "An ordinal classification for the families of flowering plants," the paper appeared in the Annals of the Missouri Botanical Garden (volume 85, pages 531–553) and recognized 40 putatively monophyletic orders encompassing 462 families. This system prioritized monophyly over traditional morphological groupings, drawing primarily from analyses of molecular data such as rbcL and 18S rDNA sequences, supplemented by morphological and anatomical evidence. It departed from earlier classifications like those of Cronquist (1981) or Takhtajan (1987) by avoiding paraphyletic taxa and introducing informal higher-level clades to reflect phylogenetic relationships without rigid ranks.^[2] A hallmark of APG I was the identification of early-diverging angiosperms as a paraphyletic "grade" rather than a formal clade, termed the ANITA grade after its components: Amborella (as a separate lineage), Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileyales. These basal groups were positioned outside the core radiation of angiosperms, challenging prior views that placed them within subclasses like Magnoliidae. The classification eliminated such traditional subclasses (e.g., Magnoliidae, Hamamelidae, and Caryophyllidae) in favor of monophyletic assemblages, recognizing core eudicots (tricolpate pollen-bearing eudicots with five key orders: Berberidopsidales, Buxales, Proteales, Ranunculales, and Trochodendrales) as a major clade. Within eudicots, it further delineated eurosids (encompassing fabids and malvids) and euasterids (campanulids and lamiids), informal names for robustly supported subclades that unified disparate families previously scattered across orders. Additionally, 25 families were listed as being of uncertain position due to insufficient data, highlighting the system's provisional nature.^[2] Despite its innovations, APG I was constrained by the limited availability of molecular data at the time, with many sequences covering only a fraction of angiosperm diversity and relying on single-gene phylogenies that lacked resolution for deeper nodes. This led to unstable placements for certain lineages, such as Proteales, which was tentatively allied with core eudicots but with weak support. The authors emphasized that the classification was not final, intended to evolve with accumulating evidence, and encouraged ongoing research to resolve uncertainties. These limitations underscored the transitional role of APG I in bridging morphological and molecular systematics.^[2]

APG II (2003)

The Angiosperm Phylogeny Group II (APG II) classification, published in 2003, built upon the foundational framework established in APG I by incorporating additional phylogenetic evidence and introducing greater flexibility in taxonomic circumscriptions.^[15] This update expanded the number of recognized orders from 40 in APG I to 45, with five newly adopted orders—Austrobaileyales, Canellales, Gunnerales, Crossosomatales, and Celastrales—reflecting improved resolution of basal angiosperm relationships.^[15] The system maintained a focus on monophyletic groups while addressing criticisms of APG I's perceived rigidity by permitting optional segregate families, allowing users to choose between broader (lumped) or narrower (split) circumscriptions based on specific needs, such as in floristic or herbarial applications.^[15] A key innovation in APG II was the broader sampling of molecular data, incorporating additional genes such as atpB alongside rbcL and matK to enhance phylogenetic accuracy across a wider range of taxa.^[15] This expanded dataset supported the formal recognition of euasterids I (encompassing Lamiales and Solanales) and euasterids II (including Asterales and Apiales) as distinct subclades within the asterids, providing clearer delineation of evolutionary relationships in this diverse group.^[15] The classification introduced nine optional segregate families to accommodate ongoing uncertainties, exemplified by the potential splitting of Barbeuiaceae and Gisekiaceae from Caryophyllaceae, which allowed for refined categorizations without disrupting the core monophyletic structure.^[15] To further promote usability, APG II emphasized optional ranks at the family level, such as the choice between recognizing Berberidaceae in a strict sense or lumping it with related taxa like Podophyllaceae, thereby responding directly to critiques that APG I mandated inflexible changes unsuitable for all taxonomic contexts.^[15] Overall, these refinements integrated post-1998 literature and molecular studies, fostering a more adaptable system that balanced phylogenetic rigor with practical taxonomy.^[15]

APG III (2009)

The Angiosperm Phylogeny Group III (APG III) classification was published in the Botanical Journal of the Linnean Society in 2009, representing a significant update to the APG II system by incorporating advances in molecular phylogenetic data. This iteration reduced the number of recognized families from 457 in APG II to 413, primarily through the lumping of optional segregate families into broader, more stable circumscriptions to promote consensus in taxonomic practice. For example, within Dipsacales, families such as Diervillaceae were merged into Caprifoliaceae to eliminate provisional segregates. The classification maintained 59 orders, emphasizing monophyly based on robust phylogenetic evidence while avoiding the proliferation of small families that had characterized earlier systems.^[12] Key phylogenetic updates in APG III reflected stronger support for certain clades derived from expanded datasets. Notably, the commelinids received enhanced resolution, with improved branching patterns within this monocot group due to denser sampling and multi-gene analyses. Additionally, Chloranthaceae was elevated to its own order, Chloranthales, and positioned as sister to the magnoliids, clarifying its placement among early-diverging angiosperms and resolving ambiguities from prior classifications. These changes eliminated most of the optional family treatments from APG II, favoring a single, preferred hierarchy to enhance stability and usability in floristic and systematic works.^[12] Advancements in data generation underpinned these revisions, including the incorporation of expressed sequence tag (EST) data alongside traditional chloroplast and nuclear markers, which provided deeper insights into gene evolution and relationships. Increased taxon sampling across angiosperms—encompassing thousands of species—helped resolve previous polytomies, particularly in basal lineages and within major orders, yielding more confident tree topologies. By building on the optional segregates introduced in APG II, APG III prioritized a streamlined system that balanced phylogenetic accuracy with practical taxonomy.^[12]

APG IV (2016)

The APG IV classification represents the fourth major update to the Angiosperm Phylogeny Group system, published in the Botanical Journal of the Linnean Society in 2016. This revision recognizes a total of 64 orders and 416 families of flowering plants, expanding from the previous iteration by incorporating findings from numerous phylogenetic studies conducted since 2009. Key changes include the formal recognition of five new orders—Boraginales, Dilleniales, Icacinales, Metteniusales, and Vahliales—based on robust molecular evidence that resolves their distinct evolutionary positions.^[16] A notable innovation in APG IV is the proposal of two new informal superclades: superrosids and superasterids, which encompass additional orders branching from the core rosid and asterid lineages, respectively, to better reflect broader phylogenetic patterns. For instance, the order Boraginales is newly established to accommodate Boraginaceae and related families previously included in Lamiales, supported by multi-locus analyses demonstrating their basal position within lamiids. The update also relocates several parasitic families to more precise positions, such as Cynomoriaceae within Saxifragales, drawing on expanded nuclear and plastid data to clarify relationships among holoparasites. These refinements emphasize the integration of diverse molecular datasets, including emerging genomic sequences, to strengthen support for deep-level nodes in the angiosperm tree.^[17] APG IV achieves a high degree of completeness at the family level, with nearly all 416 families placed in orders with strong phylogenetic support from bootstrap values exceeding 50% or Bayesian posterior probabilities above 0.95 in large-scale analyses. Unlike earlier versions, it eliminates major optional placements, leaving only a single genus of uncertain position, thereby providing a stable framework for angiosperm taxonomy that addresses most family-level relationships comprehensively. This update builds briefly on resolutions from APG III by incorporating post-2009 studies to refine unstable nodes without introducing significant lumping or splitting beyond evidence-based necessities.^[18]

Impact and Legacy

Influence on Global Classifications

The Angiosperm Phylogeny Group (APG) classifications have been widely adopted as the standard framework for organizing angiosperm taxonomy in major international herbaria and databases. For instance, the Missouri Botanical Garden maintains the Angiosperm Phylogeny Website, which explicitly implements the APG system to characterize all orders and families of extant angiosperms, facilitating research and curation activities.^[19] Similarly, the Royal Botanic Gardens, Kew, integrates APG classifications into its systematic botany efforts, recognizing it as a consensus-based approach that resolves longstanding ambiguities in flowering plant relationships.^[20] This adoption extends to collaborative digital resources like World Flora Online, which uses the APG IV classification as a core component of its taxonomic backbone for documenting global plant diversity.^[21] The APG systems have significantly influenced conservation assessments, including those for the IUCN Red List of Threatened Species, by providing a phylogenetically informed structure for evaluating extinction risks among angiosperms. Studies predicting global extinction risks for flowering plants, for example, rely on APG classifications to categorize taxa and analyze phylogenetic diversity in threat patterns, ensuring assessments align with evolutionary relationships rather than outdated morphological groupings.^[22] This integration helps prioritize conservation actions for clades at higher risk, such as those in rapidly diversifying orders like Asterales. In comparison to earlier systems, the APG framework has largely superseded pre-molecular classifications like that of Takhtajan (1997), which recognized far more orders (232 versus APG's 40 in early versions) based on morphological traits alone.^[23] Unlike Takhtajan's strictly ranked hierarchy, APG allows for unranked clades to better reflect phylogenetic evidence from DNA sequence data, promoting flexibility in accommodating new discoveries without rigid Linnaean constraints.^[13] The ongoing impact of APG is evident in its role as the foundational scaffold for large-scale species-level phylogenies and genomic initiatives. For example, the dated angiosperm phylogeny in Zanne et al. (2014), encompassing over 30,000 species, was constructed using Phylomatic software calibrated to the APG III framework, enabling analyses of evolutionary traits like woodiness and freezing tolerance across the tree of life. As of 2025, no major APG V update has been released, with APG IV (2016) remaining the current standard; however, it continues to inform projects like Angiosperms353, a probe set targeting 353 nuclear genes across all APG-defined families to resolve genus-level relationships and support phylogenomic research.^[24]

Membership and Collaboration

The Angiosperm Phylogeny Group (APG) originated in 1998 as an informal international collaboration among approximately 40 systematic botanists specializing in molecular phylogenetics, aimed at synthesizing emerging DNA-based evidence into a consensus classification of flowering plants. Led by Mark W. Chase of the Royal Botanic Gardens, Kew, and Peter F. Stevens of the University of Missouri, the founding effort produced the inaugural APG I system, which emphasized monophyletic groupings derived from multigene analyses.^[2]^[20] Other key founding members included Michael F. Fay from Kew, who contributed expertise in molecular systematics and taxonomic revision.^[25]^[20] The APG's collaborative process relies on decentralized, consensus-driven mechanisms rather than a formal structure, including informal workshops, email exchanges, and targeted discussions among experts to integrate molecular, morphological, and anatomical data. This approach promotes inclusivity by inviting contributions from specialists in molecular systematics worldwide, avoiding rigid hierarchies and allowing iterative refinements based on new evidence. For instance, updates like APG II (2003) and APG III (2009) emerged from similar ad hoc gatherings and correspondence, ensuring broad input while maintaining focus on phylogenetic accuracy.^[12] Leadership within the group rotates informally among core participants to distribute responsibilities for compiling updates and coordinating input, fostering sustained engagement across iterations. The APG IV system (2016), for example, was coordinated by a team of 10 compilers including Chase, Stevens, Fay, and Douglas E. Soltis, with 15 additional contributors providing specialized reviews.^[13]^[18] As of 2025, the APG maintains a core of 20-30 active members, drawing from global institutions such as the Royal Botanic Gardens, Kew, the Missouri Botanical Garden, and various university herbaria, to monitor ongoing genomic advancements and prepare potential future revisions. This enduring network underscores the group's role in bridging international expertise for evolutionary plant classification.^[20]^[19]

References

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Mar 27, 2019 · The broad assessments of angiosperm relationships proposed by Cronquist ... paraphyletic, although neither the concept of paraphyly nor its ...
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For these reasons, the rbcL gene appeared to offer an excellent molecule for the estimation of flowering plant phy- logenies. To facilitate a coordinated effort.
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Apr 1, 2011 · In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. • Methods: ...
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We follow these principles here. Backlund and Bremer's main principle is that taxa that are recognized formally should be monophyletic. However, this does ...
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update of the Angiosperm Phylogeny Group classification for the ...
An update of the Angiosperm Phylogeny Group (APG) classification of the orders and families of angiosperms is presented. Several new orders are recognized: ...
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update of the Angiosperm Phylogeny Group classification for the ...
The initial APG (1998) system comprised 462 families arranged in 40 putatively monophyletic orders and a few monophyletic higher groups. The latter were named ...
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An update of the Angiosperm Phylogeny Group classification for the ...
Apr 18, 2016 · This brings the total number of orders and families recognized in the APG system to 64 and 416, respectively.
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An update of the Angiosperm Phylogeny Group classification for the ...
Apr 6, 2016 · Two parasitic families formerly of uncertain positions are now placed: Cynomoriaceae in Saxifragales and Apodanthaceae in Cucurbitales. ... APG IV ...
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Jul 22, 2021 · Angiosperms353 is a target sequence capture probe set designed to work across all angiosperm families, targeting 353 genes.
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