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Phylogenetic Pattern, Diversity, and Diversification of Eudicots
Abstract
The implementation of explicit phylogenetic techniques to the study of relationships among angiosperms has led to the recognition of a major monophyletic group, the eudicot clade, characterized by the production of tricolpate or tricolpate-derived pollen grains. Eudicots comprise nearly 75% of extant angiosperm species (subclasses Hamamelididae, Caryophyllidae. Dilleniidae, Rosidae, and Asteridae, as well as the order Ranunculales in the Magnoliidae sensu Cronquist). Recent phylogenetic analyses, based on both morphological data and molecular sequences, have begun to clarify higher-level phylogenetic relationships within the eudicot clade. The basalmost branch within the eudicots separates a small ranunculid clade, which includes the Ranunculales and Papaverales. The main group within the eudicots, here referred to as the main cudicot clade, is formed by a basal grade of species-poor lineages, mostly of "lower" Hamamelididae, and a large monophyletic group, here referred to as core eudicots, which includes ca. 97% of eudicot species diversity. Within the core eudicots, three distinct groups can be recognized. (1) The caryophyllid clade (ca. 6% of eudicot species diversity) includes the Caryophyllidae as traditionally defined and a few additional taxa previously thought to be of dilleniid and rosid affinity. (2) The rosid clade (ca. 39% of total eudicot species diversity) is composed mostly of taxa previously included in Dilleniidae and Rosidae, and includes a well-supported clade that we term here the core rosids (ca. 24% of total eudicot species diversity). Among the taxa in the core rosid clade are the Fabaceae, Rosaceae, Linales, and Cunoniaceae, as well as some families of Violales, and the "higher" Hamamelididae. (3) The asterid clade (ca. 50% of eudicot species diversity) consists of two large clades composed mostly of taxa previously assigned to Asteridae, and additional members of Rosidae and Dilleniidae. One of these large asterid clades is dominated by the Asterales s.l. (ca. 17% of total eudicot species diversity), while the other corresponds to a broadly defined Lamiidae (ca. 26% of total eudicot species diversity). Paleobotanical data first document the presence of early cudicots ca. 125 million years before the present (Barremian-Aptian boundary, Lower Cretaceous), prior to the major diversification and ecological radiation of angiosperms. Well-preserved floral remains and other fossils provide a minimum age for the origin of eudicot lineages. Sediments of Albian age contain floral remains of Platanaceae and probable Buxaceae, both of which fall within the species-poor lineages at the base of the main eudicot clade. In slightly younger sediments, the taxonomic diversity of eudicots increases considerably. Basal taxa in the core eudicots are represented by Hamamelidaceae and by several flowers of broad saxifragalean affinity in Turonian-Campanian strata. Among taxa within the rosid clade, the Capparales and Myrtales are documented from the Turonian and Santonian-Campanian, respectively. The core rosids are represented by several flowers with affinities to Juglandales, Myricales, and Fagales in the Santonian-Campanian. Flowers with possible affinities to Hydrangeaceae, from the Coniacian-Santonian, represent the basalmost group within the asterid clade, and flowers of broad ericalean affinity (including Actinidiaceae), from the Turonian-Campanian, document the presence of several groups within the ericalean clade. The Asteridae s.l. are not securely represented in the Upper Cretaceous, and, to our knowledge, there is no reliable Cretaceous record for any member of the Lamiidae s.l. Although nearly all of the main eudicot clades are represented by at least one of their included lineages in the Upper Cretaceous, the earliest well-documented records of the Fabaceae, Asteraceae, Lamiales s.l., and Gentianales, which together comprise ca. 45% of total eudicot species diversity, are found in uppermost Cretaceous (Maastrichtian) or Tertiary sediments. The three subfamilies of Fabaceae are well documented by flowers and fruits in the Eocene, although the presence of pollen grains assigned to Caesalpinioideae from Maastrichtian strata suggests that the family extends back into the uppermost Cretaceous. The Asteraceae, Lamiales s.l., and Gentianales are known from the Paleogene based mostly on vegetative remains. The uneven distribution of species diversity among the major clades of eudicots, and the fact that the most species-rich groups are known only from relatively young fossils, suggests that a significant portion of eudicot diversity is the result of relatively recent radiations that occurred during the second half of angiosperm evolutionary history. The evolutionary basis for the explosive diversification of specific eudicot clades-in terms of exceptionally high speciation rates, low extinction rates, or both-remains uncertain.
... The basal position of the Platanaceae in Eudicots makes the family very important in the systematics of Eudicots [9][10][11][12]. The extant Platanaceae includes only one genus, Platanus, with 7-9 species scattered in the temperate to tropical regions of North America, Europe as well as southeastern Asia [12,13]. ...
... The diversity of the family used to be much greater than today [14][15][16][17]. Their fossil record starts from the Early Cretaceous, and is widely distributed in Greenland, Europe, North America, and Asia [10,11,13,. The oldest record goes back to the Aptian [36], but the records become abundant since the Albian [9,17,22,23,[29][30][31][32][33]35,37]. ...
Angiosperms and insects are two most diverse groups of macroscopic organisms, and their relationship plays an important role in the current ecosystem. An angiosperm is usually attacked by multiple insects in the current ecosystem, which is a proxy of the complication of the ecosystem. However, such a complicate relationship appears lacking in the ecosystem for early angiosperms, which are usually attacked by only one type of insects. Therefore, when the complicate angiosperm-related ecosystem emerged is an important unanswered question. Here we document a new platanaceous species, Arthollia dayangshuensis gen. et sp. nov from the Nenjiang Formation (late Santonian-early Campanian, Late Cretaceous) with three different kinds of damages, suggesting that the ecological relationship between angiosperms and insects was already complicate in the Santonian. This surprising discovery implies that angiosperm-related ecosystem has already existed in the Late Cretaceous. To this date, this is the first sign of such a complicating process.
... Concordant with fossil evidence [56,57,59,60,62,69,86], which suggests that the early evolution of the WCS might have experienced radiative lineage diversification, the results of divergence time estimation indicated that the WCS underwent rapid divergence in the crown groups during the early Cretaceous, leading to the occurrence of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (within ∼4.56 Ma, and between 104.79 and 100.23 Ma). The mutually supporting evidence suggests that, in addition to ancient hybridization, incomplete lineage sorting (the stochastic sorting of ancestral sequence polymorphisms) [16,51] resulted from the process of radiative diversification during the early evolution of WSC may contribute to the observed phylogenetic recalcitrance in the deep relationships of the WCS. ...
Background The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence. Results Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected. Conclusions Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/ Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.
... Concordant with fossil evidence [56,57,59,60,62,69,86], which suggests that the early evolution of the WCS might have experienced radiative lineage diversification, the results of divergence time estimation indicated that the WCS underwent rapid divergence in the crown groups during the early Cretaceous, leading to the occurrence of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (within ∼4.56 Ma, and between 104.79 and 100.23 Ma). The mutually supporting evidence suggests that, in addition to ancient hybridization, incomplete lineage sorting (the stochastic sorting of ancestral sequence polymorphisms) [16,51] resulted from the process of radiative diversification during the early evolution of WSC may contribute to the observed phylogenetic recalcitrance in the deep relationships of the WCS. ...
Background
The “woody clade” in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence.
Results
Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected.
Conclusions
Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.
... In terms of trait combinations, the most common flower is bisexual, with a differentiated perianth arranged in two whorls (45% of living species in our dataset). These traits characterize Pentapetalae, the angiosperm clade containing > 70% of extant species (Magallon et al., 1999;Christenhusz & Byng, 2016). For the flower, the higher occupation of some areas of the morphospace can be attributed to the economy of construction and/or to functional advantages (Stebbins, 1951;Endress, 1982). ...
Flowers are the complex and highly diverse reproductive structures of angiosperms. Because of their role in sexual reproduction, the evolution of flowers is tightly linked to angiosperm speciation and diversification. Accordingly, the quantification of floral morphological diversity (disparity) among angiosperm subgroups and through time may give important insights into the evolutionary history of angiosperms as a whole.
Based on a comprehensive dataset focusing on 30 characters describing floral structure across angiosperms, we used 1201 extant and 121 fossil flowers to measure floral disparity and explore patterns of floral evolution through time and across lineages.
We found that angiosperms reached their highest floral disparity in the Early Cretaceous. However, decreasing disparity toward the present likely has not precluded the innovation of other complex traits at other morphological levels, which likely played a key role in the outstanding angiosperm species richness.
Angiosperms occupy specific regions of the theoretical morphospace, indicating that only a portion of the possible floral trait combinations is observed in nature. The ANA grade, the magnoliids, and the early‐eudicot grade occupy large areas of the morphospace (higher disparity), whereas nested groups occupy narrower regions (lower disparity).
... The rosids is one of the most diverse lineages of flowering plants, containing 17 orders, which in turn comprise 140 families and ca. 70,000 species, exhibiting remarkable morphological and ecological diversities (APG II, 2003;APG III, 2009;Chase et al., 1993;Magallon et al., 1999). The rosids consists of an unusually heterogeneous group with respect to habitat and life form, with member species occurring as herbs, trees, aquatics and succulents. ...
The Rosids is one of the largest groups of flowering plants, with 140 families and 70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from nuclear genes. To better understand the evolutionary history of rosids, it is necessary to investigate their phylogenetic relationships using nuclear genes. Here, we employed large-scale phylogenomic datasets composed of nuclear genes, including 891 clusters of putative orthol-ogous genes. Combined with comprehensive taxon sampling covering 63 species representing 14 out of the 17 orders, we reconstructed the rosids phylogeny with coalescence and concatenation methods, yielding similar tree topologies from all datasets. However, these topologies did not agree on the placement of Zygophyllales. Through comprehensive analyses, we found that missing data and gene tree heterogeneity were potential factors that may mislead concatenation methods, in particular, large amounts of missing data under high gene tree heterogeneity. Our results provided new insights into the deep phylogenetic relationships of the rosids, and demonstrated that coalescence methods may effectively resolve the phylogenetic relationships of the rosids with missing data under high gene tree heterogeneity.
Benzoxazinoids (BXDs) are important defense compounds produced by a number of species from different, evolutionarily unrelated plant families. While BXD biosynthesis has been extensively studied in the grasses (monocots) and core eudicots, the mechanism of BXD synthesis in the basal eudicots is still unclear. We used an integrated metabolomics and transcriptomics approach to elucidate the BXD pathway in Consolida orientalis, a Ranunculaceae species known to produce the BXD DIBOA-Glc. Overexpression of candidate genes in Nicotiana benthamiana identified a flavin-dependent monooxygenase (CoBX2-3) and two cytochrome P450 enzymes (CoBX4 and CoBX5) that catalyze the oxidation steps that transform indole into DIBOA. Co-expression of CoBx2-3, CoBx4, and CoBx5 with the previously described indole synthase gene CoBx1 and the UDP-glucosyltransferase gene CoBx8 in N. benthamiana resulted in the reconstitution of a fully active BXD pathway. The fact that CoBX2-3, CoBX4, and CoBX5 are not phylogenetically related to their counterparts in the grasses and core eudicots suggests independent evolution of benzoxazinoid biosynthesis in these three angiosperm lineages.
The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental disjunct distribution, Fraxinus was used as a model organism to integrate abundant fossil evidence with high-resolution phylogenies in a phytogeographic analysis. We constructed a robust phylogenetic tree using genomic data, reconstructed the geographic ancestral areas, and evaluated the effect of incorporating fossil information on the reconstructed biogeographic history. The phylogenetic relationships of Fraxinus were highly resolved and divided into seven clades. Fraxinus originated in western North America during Eocene, and six intercontinental dispersal events and five intercontinental vicariance events were occured. Results suggest that climate change and vicariance contributed to the intercontinental disjunct distribution pattern of Fraxinus. Moreover, results highlight the necessity of integrating phylogenetic relationship and fossil to improve the reliability of inferred biogeographic events and our understanding of the processes underlying disjunct distributions.
Background & Aim:
Pollen grain is an important component for c arrying and spreading plant genetic information. It
contains the key code of angiosperm biodiversity, which can provide a micromorphological view for exploring
“Darwin s abominable mystery Pollen morphology is hereditary and highly diverse in angiosperms and has been used
to study plant classification, evolution, ecology, biogeography and so on. However, current studies mainly focus on
pollen shape, size, aperture, surface ornamentation, and microspore formation and development, and ignore pollen
color. W e intend to review the research on pollen color in a ngiosperms a nd suggest further stud ies
Progress:
Previous studies have outlined the chemical and genetic bases of pollen color, including biological factors
(pollinator preference, visual crypsis, dimo rphic selection, etc.) and abiotic factors (ultraviolet, temperature, humidity,
latitude and longitude, etc.). Researchers have also introduced the practical applications for the understanding pollen
color in apiology, plant tissue culture techniques, food science, horticulture and other related fields. We summarized the
pollen color data reported in the last hundred years, which contains 47 families and 7 1 genera of angiosperms. We inferred
the evolutionary pattern s of pollen color using the Fitch parsimony method.
The plant fossil record during the Cretaceous documents a major transition in the dominant group of terrestrial autotrophs, as plant communities from the earlier Mesozoic were transformed by the appearance and rapid diversification of angiosperms. This transformation began in the Early Cretaceous, continued through the Late Cretaceous, and led ultimately to the dominance of angiosperm in most terrestrial ecosystems today, which had profound consequences for the other organisms inhibiting terrestrial ecosystems and perhaps the planet as a whole. Our understanding of angiosperm diversification has been greatly improved over the past 50 years by integrated studies of fossil assemblages containing angiosperm pollen and leaves, but especially by new information from mesofossil floras that have provided previously unanticipated detail on floral form in Cretaceous angiosperms and have allowed the recognition of key dispersed pollen types in situ . Information from fossil flowers has greatly facilitated meaningful comparisons with living plants and integration with phylogenetic analyses of extant angiosperms based on DNA evidence. The combined insights from these discoveries provide a broadly consistent and coherent picture of angiosperm evolution through the Cretaceous, which comprises more than half of their entire evolutionary history.
Melatonin is produced by plants, algae, and animals. Worldwide studies show diverse positive effects of exogenous melatonin on plants, edible plant products, and algae, but the potential of melatonin to enhance food and feed systems through these positive effects remains largely unexplored. Through a meta-analysis of about 25,000 observations, we show that exogenous application of melatonin significantly increases crop productivity and yields, and enhances the nutritional and nutraceutical value of edible plant products and algae by regulating diverse biological functions. Melatonin can improve plants, edible plant products, and algae under various current climate change scenarios, environmental pollution factors, and other stresses by about 7% to nearly 30%, on average, depending on the stressor. We also analyze various technical/methodological factors influencing the desired outcomes and identify conditions that offer optimal enhancement. This study offers a scientific and technical roadmap facilitating sustainable food and feed production through the application of exogenous melatonin.
Technological advances in molecular biology have greatly increased the speed and efficiency of DNA sequencing, making it possible to construct large molecular data sets for phylogeny reconstruction relatively quickly. Despite their potential for improving our understanding of phylogeny, these large data sets also provide many challenges. In this paper, we discuss several of these challenges, including 1) the failure of a search to find the most parsimonious trees (the local optimum) in a reasonable amount of time, 2) the difference between a local optimum and the global optimum, and 3) the existence of multiple classes (islands) of most parsimonious trees. We also discuss possible strategies to improve the' likelihood of finding the most parsimonious tree(s) and present two examples from our work on angiosperm phylogeny. We conclude with a discussion of two alternatives to analyses of entire large data sets, the exemplar approach and compartmentalization, and suggest that additional consideration must be given to issues of data analysis for large data sets, whether morphological or molecular.
Nucleotide sequences from the rbcL and atpB genes (chloroplast DNA) and 18S nuclear ribosomal DNA provide important new data with which to test previous hypotheses of inter-familial relationships in the angiosperm subclass Ranunculidae. Preliminary conclusions based on cladistic analysis of the combined molecular data sets for all three genes are broadly congruent with previous analyses based on rbcL data alone. The genus Euptelea, which has been placed traditionally among the “lower” Hamamelididae, is resolved as more closely related to ranunculids. Papaverales (represented by Pteridophyllaceae and Fumariaceae including Hypecoum) are strongly supported as a monophyletic group, and are resolved as basal to all other ranunculids (“core” ranunculids) plus Euptelea. The monotypic genera Kingdonia and Circaeaster are placed as sister taxa and together are sister to Lardizabalaceae s.l. (including Sargentodoxa). The Lardizabalaceae-Circaeaster-Kingdonia clade is the sister taxon to Menispermaceae-Ranunculaceae-Berberidaceae. Menispermaceae is the sister taxon to Ranunculaceae and Berberidaceae.
The chloroplast genes atpB and rbcL and nuclear ribosomal 18S DNA were sequenced for 23 genera of the Ranunculaceae and two outgroup taxa (Hydrastis and Glaucidium). The three sequence data sets were combined and the resulting preliminary phylogenetic tree used to assess relationships within the Ranunculaceae. The phylogeny strongly supports the monophyly of the family, with 26 substitutions, a bootstrap value of 98% and a decay index of > 7. Within the family, the T-type chromosome group is basal and paraphyletic with respect to the larger R-type chromosome group. Within the T-type chromosome group, Coptis and Xanthorhiza from a monophyletic group and are basal to all other Ranunculaceae. Other alliances previously proposed by taxonomists are confirmed: Anemonella/Thalictrum/ lsopyrum/Aquilegia/Semiaquilegia; Anemone/Clematis, Trautvetteria/
Myosurus/Ranunculus; Aconitum/Delphinium; and Anemonopsis/Cimicifugal/Actaea. Other groupings that could not have been predicted on the basis of traditional data include a clade consisting of Adonis and Trollius and the inclusion of Eranthis in a clade with Anemonopsis, Cimicifuga, and Actaea. Nigella is weakly allied with a clade consisting of Aconitum and Delphinium. The molecular sequence data are largely congruent with results based on cytology, phytochemistry, and micromorphology. Flower and fruit characters are homoplastic in relation to the cladogram based on sequence data. The pattern of relationships based on sequence data supports the view that staminodia/petals and achenes have evolved independently several times within the Ranunculaceae.
The fossil occurrences of leaves and fruits assigned to the Recent genus Coriaria are critically revised. A new species - Coriaria collinsonae - is described. Ecological and stratigraphical considerations show the significance of this 'old and subtropical' element in the European Tertiary. - Author
The fossil pollen genus Aquilapollenites, which occurs in most Upper Cretaceous and some Lower Tertiary sediments from the western interior of North America, represents at least two lines of development from a Santalalean stock. One line, which approximates the isopolar forms of the genus, bears a close morphological and probably genetic relationship with the extant plant family Loranthaceae. The second line, which encompasses the heteropolar and subisopolar forms, shares affinity with some members of the Santalaceae, especially the genus Arfona. The parasitic habit of flowering plants was well developed, and was a conspicuous element within the subtropical to warm-temperate forest regions of western North America during the close of the Cretaceous and early Tertiary.