@misc{arnold1947introduction1, author = "Arnold, C. A", title = "Introduction to Paleobotany", year = "1947", howpublished = "New York, McGraw-Hill, 433 p", note = "talkorigins\_source = {true}; raw\_reference = {Arnold, C. A., 1947, Introduction to Paleobotany: New York, McGraw-Hill, 433 p.}" } @article{doi1023071943261, author = "Stebbins, G. Ledyard", title = "Evidence on Rates of Evolution from the Distribution of Existing and Fossil Plant Species", year = "1947", journal = "Ecological Monographs", url = "https://doi.org/10.2307/1943261", doi = "10.2307/1943261", openalex = "W1998160448" } @book{chaney1949evolutionary2, author = "Chaney, R. W", title = "Evolutionary trends in the angiosperms, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution", year = "1949", publisher = "Princeton, New Jersey, Princeton University Press, p. 190-201; 474 p", note = "talkorigins\_source = {true}; raw\_reference = {Chaney, R. W., 1949, Evolutionary trends in the angiosperms, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution: Princeton, New Jersey, Princeton University Press, p. 190-201; 474 p.}" } @article{doi101111j155856461952tb02810x, author = "Axelrod, Daniel I.", title = "A THEORY OF ANGIOSPERM EVOLUTION", year = "1952", journal = "Evolution", abstract = "Journal Article A THEORY OF ANGIOSPERM EVOLUTION Get access Daniel I. Axelrod Daniel I. Axelrod University of California Los Angeles Search for other works by this author on: Oxford Academic Google Scholar Evolution, Volume 6, Issue 1, 1 March 1952, Pages 29–60, https://doi.org/10.1111/j.1558-5646.1952.tb02810.x Published: 01 March 1952 Article history Received: 22 October 1951 Published: 01 March 1952", url = "https://doi.org/10.1111/j.1558-5646.1952.tb02810.x", doi = "10.1111/j.1558-5646.1952.tb02810.x", openalex = "W2320024939", references = "doi101144transglas211117" } @article{doi1023072405502, author = "Axelrod, Daniel I.", title = "A Theory of Angiosperm Evolution", year = "1952", journal = "Evolution", url = "https://doi.org/10.2307/2405502", doi = "10.2307/2405502", openalex = "W4240185923" } @inproceedings{whittaker1969evolution4, author = "Whittaker, R. H", title = "Evolution of diversity in plant communities", year = "1969", booktitle = "Brookhaven Symposium on Biology, v. 22, p. 178-196", note = "talkorigins\_source = {true}; raw\_reference = {Whittaker, R. H., 1969, Evolution of diversity in plant communities: Brookhaven Symposium on Biology, v. 22, p. 178-196.}" } @incollection{banks1970angiosperms, author = "Banks, Harlan P.", title = "Angiosperms — the Culmination of Plant Evolution", year = "1970", booktitle = "Evolution and Plants of the Past", url = "https://doi.org/10.1007/978-1-349-01818-5\_9", doi = "10.1007/978-1-349-01818-5\_9", openalex = "W2482891615", pages = "147-160", references = "doi101111j155856461952tb02810x, doi101144gsljgs1923079010409, doi1023071943261, doi1023072405502, doi1023072799872, doi105962bhltitle110147, openalexw1560240034" } @article{doi1023071218350, author = "Cronquist, Arthur and Stebbins, G. Ledyard", title = "Flowering Plants. Evolution above the Species Level", year = "1975", journal = "Taxon", url = "https://doi.org/10.2307/1218350", doi = "10.2307/1218350", openalex = "W1589280229" } @article{doi1023072418725, author = "Thorne, Robert F. and Beck, Charles B.", title = "Origin and Early Evolution of Angiosperms.", year = "1976", journal = "Systematic Botany", url = "https://doi.org/10.2307/2418725", doi = "10.2307/2418725", openalex = "W1981841294" } @article{doi101111j1469185x1977tb01347x, author = "Grubb, P. J.", title = "THE MAINTENANCE OF SPECIES‐RICHNESS IN PLANT COMMUNITIES: THE IMPORTANCE OF THE REGENERATION NICHE", year = "1977", journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society", abstract = "SUMMARY According to ‘Gause's hypothesis’ a corollary of the process of evolution by natural selection is that in a community at equilibrium every species must occupy a different niche. Many botanists have found this idea improbable because they have ignored the processes of regeneration in plant communities. Most plant communities are longer‐lived than their constituent individual plants. When an individual dies, it may or may not be replaced by an individual of the same species. It is this replacement stage which is all‐important to the argument presented. Several mechanisms not involving regeneration also contribute to the maintenance of species‐richness: differences in life‐form coupled with the inability of larger plants to exhaust or cut off all resources, also the development of dependence‐relationships, differences in phenology coupled with tolerance of suppression, fluctuations in the environment coupled with relatively small differences in competitive ability between many species, the ability of certain species‐pairs to form stable mixtures because of a balance of intraspecific competition against interspecific competition, the production of substances more toxic to the producer‐species than to the other species, differences in the primary limiting mineral nutrients or pore‐sizes in the soil for neighbouring plants of different soecies, and differences in the competitive abilities of species dependent on their physiological age coupled with the uneven‐age structure of many populations. The mechanisms listed above do not go far to explain the indefinite persistence in mixture of the many species in the most species‐rich communities known. In contrast there seem to be almost limitless possibilities for differences between species in their requirements for regeneration, i.e. the replacement of the individual plants of one generation by those of the next. This idea is illustrated for tree species and it is emphasized that foresters were the first by a wide margin to appreciate its importance. The processes involved in the successful invasion of a gap by a given plant species and some characters of the gap that may be important are summarized in Table 2. The definition of a plant's niche requires recognition of four components: the habitat niche, the life‐form niche, the phenological niche, and the regeneration niche. A brief account is given of the patterns of regeneration in different kinds of plant community to provide a background for studies of differentiation in the regeneration niche. All stages in the regeneration‐cycle are potentially important and examples of differentiation between species are given for each of the following stages: Production of viable seed (including the sub‐stages of flowering, pollination and seed‐set), dispersal, in space and time, germination, establishment, and further development of the immature plant. In the concluding discussion emphasis is placed on the following themes: the kinds of work needed in future to prove or disprove that differentiation in the regeneration niche is the major explanation of the maintenance of species‐richness in plant communities, the relation of the present thesis to published ideas on the origin of phenological spread, the relevance of the present thesis to the discussion on the presence of continua in vegetation, the co‐incidence of the present thesis and the emerging ideas of evolutionists about differentiation of angiosperm taxa, and the importance of regeneration‐studies for conservation.", url = "https://doi.org/10.1111/j.1469-185x.1977.tb01347.x", doi = "10.1111/j.1469-185x.1977.tb01347.x", openalex = "W2119259345", references = "doi101038242344a0, doi101086282070, doi101086282687, doi101093biomet3812196, doi101111j155856461969tb03489x, doi101126science1473655250, doi1015159780691206912, doi1023071218190, doi1023071929601, doi1023072256497, doi1023072258550, doi1023072989767, openalexw1532540194" } @article{doi101007bf02806171, title = "Evolution and classification of flowering plants", year = "1979", journal = "Brittonia", url = "https://doi.org/10.1007/bf02806171", doi = "10.1007/bf02806171", openalex = "W1589755459" } @article{doi101007bf02861082, author = "Doyle, James A. and Donoghue, Michael J.", title = "Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach", year = "1986", journal = "The Botanical Review", url = "https://doi.org/10.1007/bf02861082", doi = "10.1007/bf02861082", openalex = "W2063845391", references = "doi101007bf02858880, doi101126science2314734129, doi1023072413454, doi105962bhltitle118957, openalexw3126336940" } @article{doi1023072418914, author = "Keener, Carl S. and Cronquist, Arthur", title = "The Evolution and Classification of Flowering Plants.", year = "1989", journal = "Systematic Botany", abstract = "The evolution and classification of flowering plants, The evolution and classification of flowering plants, مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی", url = "https://doi.org/10.2307/2418914", doi = "10.2307/2418914", openalex = "W3020856028" } @misc{freidman1990double3, author = "Freidman, W. E", title = "Double fertilization in Ephedra, a nonflowering plant; its bearing on the origin of angiosperms", year = "1990", howpublished = "Science, v. 247, p. 951", note = "talkorigins\_source = {true}; raw\_reference = {Freidman, W. E., 1990, Double fertilization in Ephedra, a nonflowering plant; its bearing on the origin of angiosperms: Science, v. 247, p. 951.}" } @article{doi101073pnas89167844, author = "Bousquet, Jean and Strauss, Steven H. and Doerksen, Allan H. and Price, Robert A.", title = "Extensive variation in evolutionary rate of rbcL gene sequences among seed plants.", year = "1992", journal = "Proceedings of the National Academy of Sciences", abstract = "Extensive variation in synonymous and nonsynonymous rates of substitution was observed among 50 sequences of the gene coding for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) representing bryophyte, conifer, dicot, and monocot taxa. Relative rate tests revealed rate differences of up to 138\% for nonsynonymous substitutions and up to 85\% for synonymous ones. Within angiosperms, the annual forms evolved more rapidly, on average, than perennial forms. This rate heterogeneity was more extensive at nonsynonymous sites than synonymous ones, and it resulted primarily from a recent acceleration of substitution rate in many groups of angiosperms.", url = "https://doi.org/10.1073/pnas.89.16.7844", doi = "10.1073/pnas.89.16.7844", openalex = "W1968683533" } @article{doi101086417659, author = "Herms, Daniel A. and Mattson, William J.", title = "The Dilemma of Plants: To Grow or Defend", year = "1992", journal = "The Quarterly Review of Biology", abstract = "Physiological and ecological constraints play key roles in the evolution of plant growth patterns, especially in relation to defenses against herbivores. Phenotypic and life history theories are unified within the growth-differentiation balance (GDB) framework, forming an integrated system of theories explaining and predicting patterns of plant defense and competitive interactions in ecological and evolutionary time. Plant activity at the cellular level can be classified as growth (cell division and enlargement) of differentiation (chemical and morphological changes leading to cell maturation and specialization). The GDB hypothesis of plant defense is premised upon a physiological trade-off between growth and differentiation processes. The trade-off between growth and defense exists because secondary metabolism and structural reinforcement are physiologically constrained in dividing and enlarging cells, and because they divert resources from the production of new leaf area. Hence the dilemma of plants: They must grow fast enough to complete, yet maintain the defenses necessary to survive in the presence of pathogens and hervivores. The physiological trade-off between growth and differentiation processes interacts with herbivory and plant-plant competition to manifest itself as a genetic trade-off between growth and defense in the evolution of plant life history strategies. Evolutionary theories of plant defense are reviewed. We also extend a standard growth rate model by separating its ecological and evolutionary components,and formalizing the role of competition in the evolution of plant defense. We conclude with a conceptual model of the evolution of plant defense in which plant physioligical trade-offs interact with the abiotic environment, competition and herbivory.", url = "https://doi.org/10.1086/417659", doi = "10.1086/417659", openalex = "W1990151103", references = "doi101007bf02860717, doi101086283244, doi101086284531, doi101111j109583121989tb00492x, doi101111j155856461964tb01674x, doi101111j155856461985tb00391x, doi101126science12933611466, doi101126science1713973757, doi101126science188418319, doi101126science2304728895, doi101146annureves19110188000551, doi1023071942495, doi1023072259845, doi1023072389364, openalexw2169917233" } @article{doi101098rspb19960088, author = "Barraclough, Timothy G. and Harvey, Paul and Nee, Sean", title = "Rate of rbc L gene sequence evolution and species diversification in flowering plants (angiosperms)", year = "1996", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "In sister taxa comparisons, there is a significant, positive correlation between the rate of evolution of the rbc L chloroplast gene within families of flowering plants (angiosperms), and the number of species in those families. We briefly discuss alternative evolutionary scenarios which may have generated this relation between species diversification and molecular evolution in flowering plants.", url = "https://doi.org/10.1098/rspb.1996.0088", doi = "10.1098/rspb.1996.0088", openalex = "W2121360952", references = "doi101006mpev19931009, doi101038355511a0, doi101073pnas89167844, doi101098rspb19950031, doi101111j109600311989tb00482x, doi101146annureves22110191001433, doi1023071222465, doi1023072399846, doi1023074109916" } @article{doi1023072992015, title = "An Ordinal Classification for the Families of Flowering Plants", year = "1998", journal = "Annals of the Missouri Botanical Garden", abstract = "Recent cladistic analyses are revealing the phylogeny of flowering plants in increasing detail, and there is support for the monophyly of many major groups above the family level.With many elements of the major branching sequence of phylogeny established, a revised suprafamilial classification of flowering plants becomes both feasible and desirable.Here we present a classification of 462 flowering plant families in 40 putatively monophyletic orders and a small number of monophyletic, informal higher groups.The latter are the monocots, commelinoids, eudicots, core eudicots, rosids including eurosids I and II, and asterids including euasterids I and II.Under these informal groups there are also listed a number of families without assignment to order.At the end of the system is an additional list of families of uncertain position for which no firm data exist regarding placement anywhere within the system.Why rearrange families, still less formalize orders?Higher-level classifications, the grouping of species into families, orders, etc., are needed as reference tools not only in systematics but also in many other branches of biology.Knowledge of phylogenetic relationships of major groups of organisms, that is, a phylogenetic perspective, is becoming increasingly important, and hence the need for a phylogenetic classification as a reference tool is also becoming imperative.Our primary focus is on orders with a secondary emphasis on families of flowering plants.The family is central in flowering plant systematics.For example, in studying an unknown plant we usually first identify it to family.The orders, on the other hand, have until quite recently been of little importance, either being morphologically unrecognizable or in most cases lacking any evolutionary coherence (Heywood, 1977;Merxmiiller, 1977).However, orders are useful in teaching, for studying", url = "https://doi.org/10.2307/2992015", doi = "10.2307/2992015", openalex = "W143810700" } @misc{ramsay2000angiosperms, author = "Ramsay, Margaret M.", title = "Angiosperms", year = "2000", booktitle = "Encyclopedia of Cell Technology", url = "https://doi.org/10.1002/0471250570.spi004", doi = "10.1002/0471250570.spi004" } @article{doi101111j001438202001tb00826x, author = "Magallón, Susana and Sanderson, Michael J.", title = "ABSOLUTE DIVERSIFICATION RATES IN ANGIOSPERM CLADES", year = "2001", journal = "Evolution", abstract = "The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time-homogeneous birth-and-death process that depends on the diversification rate (r) and the relative extinction rate (epsilon). A statistical analysis of the birth and death process was then used to obtain 95\% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (e = 0.0) and under a high relative extinction rate (epsilon = 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species-rich or exceedingly species-poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (epsilon = 0.9) to 0.089 (epsilon = 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole.", url = "https://doi.org/10.1111/j.0014-3820.2001.tb00826.x", doi = "10.1111/j.0014-3820.2001.tb00826.x", openalex = "W2031187632", references = "doi1010029781444313918, doi101006bojl20000380, doi1010079783642616631, doi101007bf02860537, doi101007bf02860540, doi101017s0094837300006539, doi10103846536, doi101086285258, doi101098rspb19960088, doi101098rstb19940068, doi101126science13334591105, doi101214aoms1177730285, doi1023071266137, doi1023072399030, doi1023072992015, openalexw1978269554, openalexw409616968" } @article{doi101038nature01019, author = "Diamond, Jared M.", title = "Evolution, consequences and future of plant and animal domestication", year = "2002", journal = "Nature", url = "https://doi.org/10.1038/nature01019", doi = "10.1038/nature01019", openalex = "W2128616554", references = "crossref2022quaternary, doi101002sici10969136199712145s7aiddia52233co2i, doi101038414782a, doi101086300102, doi101093acprofosobl97801995490610010001, doi101111j155856461991tb04425x, doi1023071185219, doi1023072137390, doi1023072403680, doi1023072485224, doi1023072803166, doi102307jctv301gjp" } @article{doi101046j13652435200200664x, author = "Lavorel, Sandra and Garnier, Éric", title = "Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail", year = "2002", journal = "Functional Ecology", abstract = "Summary The concept of plant functional type proposes that species can be grouped according to common responses to the environment and/or common effects on ecosystem processes. However, the knowledge of relationships between traits associated with the response of plants to environmental factors such as resources and disturbances (response traits), and traits that determine effects of plants on ecosystem functions (effect traits), such as biogeochemical cycling or propensity to disturbance, remains rudimentary. We present a framework using concepts and results from community ecology, ecosystem ecology and evolutionary biology to provide this linkage. Ecosystem functioning is the end result of the operation of multiple environmental filters in a hierarchy of scales which, by selecting individuals with appropriate responses, result in assemblages with varying trait composition. Functional linkages and trade‐offs among traits, each of which relates to one or several processes, determine whether or not filtering by different factors gives a match, and whether ecosystem effects can be easily deduced from the knowledge of the filters. To illustrate this framework we analyse a set of key environmental factors and ecosystem processes. While traits associated with response to nutrient gradients strongly overlapped with those determining net primary production, little direct overlap was found between response to fire and flammability. We hypothesize that these patterns reflect general trends. Responses to resource availability would be determined by traits that are also involved in biogeochemical cycling, because both these responses and effects are driven by the trade‐off between acquisition and conservation. On the other hand, regeneration and demographic traits associated with response to disturbance, which are known to have little connection with adult traits involved in plant ecophysiology, would be of little relevance to ecosystem processes. This framework is likely to be broadly applicable, although caution must be exercised to use trait linkages and trade‐offs appropriate to the scale, environmental conditions and evolutionary context. It may direct the selection of plant functional types for vegetation models at a range of scales, and help with the design of experimental studies of relationships between plant diversity and ecosystem properties.", url = "https://doi.org/10.1046/j.1365-2435.2002.00664.x", doi = "10.1046/j.1365-2435.2002.00664.x", openalex = "W2168173042", references = "doi1010079783642809132, doi101007bf00002772, doi101023a1004327224729, openalexw2097450069, openalexw2169917233" } @article{doi101046j14698137200200397x, author = "Brundrett, Mark", title = "Coevolution of roots and mycorrhizas of land plants", year = "2002", journal = "New Phytologist", abstract = "Here, the coevolution of mycorrhizal fungi and roots is assessed in the light of evidence now available, from palaeobotanical and morphological studies and the analysis of DNA-based phylogenies. The first bryophyte-like land plants, in the early Devonian (400 million years ago), had endophytic associations resembling vesicular-arbuscular mycorrhizas (VAM) even before roots evolved. Mycorrhizal evolution would have progressed from endophytic hyphae towards balanced associations where partners were interdependent due to the exchange of limiting energy and nutrient resources. Most mycorrhizas are mutualistic, but in some cases the trend for increasing plant control of fungi culminates in the exploitative mycorrhizas of achlorophyllous, mycoheterotrophic plants. Ectomycorrhizal, ericoid and orchid mycorrhizas, as well as nonmycorrhizal roots, evolved during the period of rapid angiosperm radiation in the Cretaceous. It is hypothesised that roots gradually evolved from rhizomes to provide more suitable habitats for mycorrhizal fungi and provide plants with complex branching and leaves with water and nutrients. Selection pressures have caused the morphological divergence of roots with different types of mycorrizas. Root cortex thickness and exodermis suberization are greatest in obllgately mycorrhizal plants, while nonmycorrhizal plants tend to have fine roots, with more roots hairs and relatively advanced chemical defences. Major coevolutionary trends and the relative success of plants with different root types are discussed. Contents Summary 275 I. Introduction 276 II. Mycorrhizal Fungi 276 III. The Dawn of Mycorrhizas 279 IV. Mycorrhizal Associations of Living and Extinct Plants 282 V. Evolution of Roots 288 VI. The Root as a Habitat for Fungi 290 VII. Mycorrhizal Evolution Trends 295 Acknowledgements 298 References 298.", url = "https://doi.org/10.1046/j.1469-8137.2002.00397.x", doi = "10.1046/j.1469-8137.2002.00397.x", openalex = "W2142191074", references = "doi101017s1464793101005735, doi10103837918, doi101146annurevearth261379" } @article{doi101111j001438202002tb00137x, author = "Forbis, Tara A. and Floyd, Sandra K. and de Queiroz, Alan", title = "THE EVOLUTION OF EMBRYO SIZE IN ANGIOSPERMS AND OTHER SEED PLANTS: IMPLICATIONS FOR THE EVOLUTION OF SEED DORMANCY", year = "2002", journal = "Evolution", abstract = "Seed dormancy plays an important role in germination ecology and seed plant evolution. Morphological seed dormancy is caused by an underdeveloped embryo that must mature prior to germination. It has been suggested that the presence of an underdeveloped embryo is plesiomorphic among seed plants and that parallel directional change in embryo morphology has occurred separately in gymnosperms and in angiosperms. We test these hypotheses using original data on embryo morphology of key basal taxa, a published dataset, and the generalized least squares (GLS) method of ancestral character state reconstruction. Reconstructions for embryo to seed ratio (E:S) using family means for 179 families showed that E:S has increased between the ancestral angiosperm and almost all extant angiosperm taxa. Species in the rosid clade have particularly large embryos relative to the angiosperm ancestor. Results for the gymnosperms show a similar but smaller increase. There were no statistically significant differences in E:S between basal taxa and any derived group due to extremely large standard errors produced by GLS models. However, differences between reconstructed values for the angiosperm ancestor and more highly nested nodes are large and these results are robust to topological and branch-length manipulations. Our analysis supports the idea that the underdeveloped embryo is primitive among seed plants and that there has been a directional change in E:S within both angiosperms and gymnosperms. Our analysis suggests that dormancy enforced by an underdeveloped embryo is plesiomorphic among angiosperms and that nondormancy and other dormancy types probably evolved within the angiosperms. The shift in E:S was likely a heterochronic change, and has important implications for the life history of seed plants.", url = "https://doi.org/10.1111/j.0014-3820.2002.tb00137.x", doi = "10.1111/j.0014-3820.2002.tb00137.x", openalex = "W2179841627", references = "doi101007bf02101694, doi10103844766, doi101093oso97801985464120010001, doi1023072529087, doi105860choice185809, doi105860choice295104, doi105860choice362164, openalexw1546962148, openalexw2506868775, openalexw3217097258" } @article{doi101046j109583392003t01100158x, author = "GROUP*, THE ANGIOSPERM PHYLOGENY", title = "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II", year = "2003", journal = "Botanical Journal of the Linnean Society", url = "https://doi.org/10.1046/j.1095-8339.2003.t01-1-00158.x", doi = "10.1046/j.1095-8339.2003.t01-1-00158.x", openalex = "W2980373194", references = "doi1023072399846" } @article{doi101098rspb20042849, author = "Davies, T. Jonathan and Savolainen, Vincent and Chase, Mark W. and Moat, Justin and Barraclough, Timothy G.", title = "Environmental energy and evolutionary rates in flowering plants", year = "2004", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates.", url = "https://doi.org/10.1098/rspb.2004.2849", doi = "10.1098/rspb.2004.2849", openalex = "W2145421207", references = "doi101098rspb19960088" } @misc{crossref2005angiosperms, title = "Angiosperms", year = "2005", booktitle = "Van Nostrand's Scientific Encyclopedia", url = "https://doi.org/10.1002/0471743984.vse0445", doi = "10.1002/0471743984.vse0445" } @article{doi101016jpalaeo200507006, author = "Friis, Else Marie and Pedersen, Kaj Raunsgaard and Crane, Peter R.", title = "Cretaceous angiosperm flowers: Innovation and evolution in plant reproduction", year = "2005", journal = "Palaeogeography Palaeoclimatology Palaeoecology", url = "https://doi.org/10.1016/j.palaeo.2005.07.006", doi = "10.1016/j.palaeo.2005.07.006", openalex = "W2001715812", references = "doi101007bf02860067, doi101007bf02860540, doi101007bf02861082, doi101016s0012821x0000159x, doi101038363342a0, doi10103846536, doi101038nature01420, doi1010719780643090149, doi1023071485834, doi1023072399030, doi1023072418725, doi1023072807789, doi105860choice323883, doi105860choice323884" } @incollection{kenrick2005angiosperms, author = "Kenrick, P.", title = "Angiosperms", year = "2005", booktitle = "Encyclopedia of Geology", url = "https://doi.org/10.1016/b978-0-08-102908-4.00202-2", doi = "10.1016/b978-0-08-102908-4.00202-2", pages = "501-510" } @article{doi101073pnas0708072104, author = "Moore, Michael J. and Bell, Charles D. and Soltis, Pamela S. and Soltis, Pamela S.", title = "Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms", year = "2007", journal = "Proceedings of the National Academy of Sciences", abstract = "Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (approximately 42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae + magnoliids as sister to a well supported clade of monocots + (Ceratophyllum + eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 +/- 4.8 and 140.3 +/- 4.8 Mya.", url = "https://doi.org/10.1073/pnas.0708072104", doi = "10.1073/pnas.0708072104", openalex = "W2114217421", references = "doi101016jpalaeo200507006, doi1023072399030, openalexw2163836228" } @article{doi101073pnas0709121104, author = "Jansen, Robert K. and Cai, Zhengqiu and Raubeson, Linda A. and Daniell, Henry and dePamphilis, Claude W. and Leebens-Mack, James and Müller, Kai and Guisinger-Bellian, Mary and Haberle, Rosemarie C. and Hansen, Anne and Chumley, Timothy W. and Lee, Seung Bum and Peery, Rhiannon M. and McNeal, Joel R. and Kuehl, Jennifer V. and Boore, Jeffrey L.", title = "Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns", year = "2007", journal = "Proceedings of the National Academy of Sciences", abstract = "Angiosperms are the largest and most successful clade of land plants with >250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements.", url = "https://doi.org/10.1073/pnas.0709121104", doi = "10.1073/pnas.0709121104", openalex = "W2127735379", references = "doi101016jpalaeo200507006, doi10108010635150290069913, doi101093bioinformatics17121246, doi101111boj12385" } @article{doi101073pnas0801962105, author = "Donoghue, Michael J.", title = "A phylogenetic perspective on the distribution of plant diversity", year = "2008", journal = "Proceedings of the National Academy of Sciences", abstract = "Phylogenetic studies are revealing that major ecological niches are more conserved through evolutionary history than expected, implying that adaptations to major climate changes have not readily been accomplished in all lineages. Phylogenetic niche conservatism has important consequences for the assembly of both local communities and the regional species pools from which these are drawn. If corridors for movement are available, newly emerging environments will tend to be filled by species that filter in from areas in which the relevant adaptations have already evolved, as opposed to being filled by in situ evolution of these adaptations. Examples include intercontinental disjunctions of tropical plants, the spread of plant lineages around the Northern Hemisphere after the evolution of cold tolerance, and the radiation of northern alpine plants into the Andes. These observations highlight the role of phylogenetic knowledge and historical biogeography in explanations of global biodiversity patterns. They also have implications for the future of biodiversity.", url = "https://doi.org/10.1073/pnas.0801962105", doi = "10.1073/pnas.0801962105", openalex = "W2064987933", references = "doi101007bf02806171, doi101126science1130880, doi1023072395199, doi1023073224530" } @incollection{leng2008angiosperms, author = "Leng, Qin and Wu, Shun-qing and Friis, Else Marie", title = "ANGIOSPERMS", year = "2008", booktitle = "The Jehol Fossils", url = "https://doi.org/10.1016/b978-012374173-8.50021-1", doi = "10.1016/b978-012374173-8.50021-1", pages = "178-179-185" } @article{doi101073pnas0811421106, author = "Antonelli, Alexandre and Nylander, Johan A. A. and Persson, Claes and Sanmartín, Isabel", title = "Tracing the impact of the Andean uplift on Neotropical plant evolution", year = "2009", journal = "Proceedings of the National Academy of Sciences", abstract = {Recent phylogenetic studies have revealed the major role played by the uplift of the Andes in the extraordinary diversification of the Neotropical flora. These studies, however, have typically considered the Andean uplift as a single, time-limited event fostering the evolution of highland elements. This contrasts with geological reconstructions indicating that the uplift occurred in discrete periods from west to east and that it affected different regions at different times. We introduce an approach for integrating Andean tectonics with biogeographic reconstructions of Neotropical plants, using the coffee family (Rubiaceae) as a model group. The distribution of this family spans highland and montane habitats as well as tropical lowlands of Central and South America, thus offering a unique opportunity to study the influence of the Andean uplift on the entire Neotropical flora. Our results suggest that the Rubiaceae originated in the Paleotropics and used the boreotropical connection to reach South America. The biogeographic patterns found corroborate the existence of a long-lasting dispersal barrier between the Northern and Central Andes, the "Western Andean Portal." The uplift of the Eastern Cordillera ended this barrier, allowing dispersal of boreotropical lineages to the South, but gave rise to a huge wetland system ("Lake Pebas") in western Amazonia that prevented in situ speciation and floristic dispersal between the Andes and Amazonia for at least 6 million years. Here, we provide evidence of these events in plants.}, url = "https://doi.org/10.1073/pnas.0811421106", doi = "10.1073/pnas.0811421106", openalex = "W2026781465", references = "doi101007978146133485919, doi101111j109583122001tb01368x, doi1011300016760620001121091uhotca23co2, doi1023073515620, doi105962bhlpart13183, openalexw3001739384" } @article{doi101073pnas0813376106, author = "Wang, Hengchang and Moore, Michael J. and Soltis, Pamela S. and Bell, Charles D. and Brockington, Samuel F. and Alexandre, Roolse and Davis, Charles C. and Latvis, Maribeth and Manchester, Steven R. and Soltis, Pamela S.", title = "Rosid radiation and the rapid rise of angiosperm-dominated forests", year = "2009", journal = "Proceedings of the National Academy of Sciences", abstract = "The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100\%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of <15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107-83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns.", url = "https://doi.org/10.1073/pnas.0813376106", doi = "10.1073/pnas.0813376106", openalex = "W2158722151", references = "doi101146annurevento53103106093304" } @article{doi101073pnas0903410106, author = "Simon, Marcelo Fragomeni and Grether, Rosaura and de Queiroz, Luciano Paganucci and Skema, Cynthia and Pennington, R. Toby and Hughes, Colin E.", title = "Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire", year = "2009", journal = "Proceedings of the National Academy of Sciences", abstract = "The relative importance of local ecological and larger-scale historical processes in causing differences in species richness across the globe remains keenly debated. To gain insight into these questions, we investigated the assembly of plant diversity in the Cerrado in South America, the world's most species-rich tropical savanna. Time-calibrated phylogenies suggest that Cerrado lineages started to diversify less than 10 Mya, with most lineages diversifying at 4 Mya or less, coinciding with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide. These plant phylogenies show that Cerrado lineages are strongly associated with adaptations to fire and have sister groups in largely fire-free nearby wet forest, seasonally dry forest, subtropical grassland, or wetland vegetation. These findings imply that the Cerrado formed in situ via recent and frequent adaptive shifts to resist fire, rather than via dispersal of lineages already adapted to fire. The location of the Cerrado surrounded by a diverse array of species-rich biomes, and the apparently modest adaptive barrier posed by fire, are likely to have contributed to its striking species richness. These findings add to growing evidence that the origins and historical assembly of species-rich biomes have been idiosyncratic, driven in large part by unique features of regional- and continental-scale geohistory and that different historical processes can lead to similar levels of modern species richness.", url = "https://doi.org/10.1073/pnas.0903410106", doi = "10.1073/pnas.0903410106", openalex = "W2151396518", references = "doi101073pnas0608361104, doi101146annurevecolsys110308120327, openalexw2611511275" } @article{doi101098rspb20081919, author = "Boyce, C. Kevin and Brodribb, Timothy J. and Feild, Taylor S. and Zwieniecki, Maciej A.", title = "Angiosperm leaf vein evolution was physiologically and environmentally transformative", year = "2009", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "The veins that irrigate leaves during photosynthesis are demonstrated to be strikingly more abundant in flowering plants than in any other vascular plant lineage. Angiosperm vein densities average 8 mm of vein per mm(2) of leaf area and can reach 25 mm mm(-2), whereas such high densities are absent from all other plants, living or extinct. Leaves of non-angiosperms have consistently averaged close to 2 mm mm(-2) throughout 380 million years of evolution despite a complex history that has involved four or more independent origins of laminate leaves with many veins and dramatic changes in climate and atmospheric composition. We further demonstrate that the high leaf vein densities unique to the angiosperms enable unparalleled transpiration rates, extending previous work indicating a strong correlation between vein density and assimilation rates. Because vein density is directly measurable in fossils, these correlations provide new access to the physiology of extinct plants and how they may have impacted their environments. First, the high assimilation rates currently confined to the angiosperms among living plants are likely to have been unique throughout evolutionary history. Second, the transpiration-driven recycling of water that is important for bolstering precipitation in modern tropical rainforests might have been significantly less in a world before the angiosperms.", url = "https://doi.org/10.1098/rspb.2008.1919", doi = "10.1098/rspb.2008.1919", openalex = "W2119610202", references = "doi101016s0065250408601191, doi101046j109583392003t01100158x, doi101073pnas0608361104, doi10108000241160310004657, doi101104pp107101352, doi101111boj12385, doi101126science24749481322, doi101146annurevarplant56032604144141, doi10230725065646, doi1023073515620, openalexw1584176508" } @article{doi101111j10958339200900996x, author = "GROUP, THE ANGIOSPERM PHYLOGENY", title = "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III", year = "2009", journal = "Botanical Journal of the Linnean Society", abstract = "A revised and updated classification for the families of flowering plants is provided. Many recent studies have yielded increasingly detailed evidence for the positions of formerly unplaced families, resulting in a number of newly adopted orders, including Amborellales, Berberidopsidales, Bruniales, Buxales, Chloranthales, Escalloniales, Huerteales, Nymphaeales, Paracryphiales, Petrosaviales, Picramniales, Trochodendrales, Vitales and Zygophyllales. A number of previously unplaced genera and families are included here in orders, greatly reducing the number of unplaced taxa; these include Hydatellaceae (Nymphaeales), Haptanthaceae (Buxales), Peridiscaceae (Saxifragales), Huaceae (Oxalidales), Centroplacaceae and Rafflesiaceae (both Malpighiales), Aphloiaceae, Geissolomataceae and Strasburgeriaceae (all Crossosomatales), Picramniaceae (Picramniales), Dipentodontaceae and Gerrardinaceae (both Huerteales), Cytinaceae (Malvales), Balanophoraceae (Santalales), Mitrastemonaceae (Ericales) and Boraginaceae (now at least known to be a member of lamiid clade). Newly segregated families for genera previously understood to be in other APG-recognized families include Petermanniaceae (Liliales), Calophyllaceae (Malpighiales), Capparaceae and Cleomaceae (both Brassicales), Schoepfiaceae (Santalales), Anacampserotaceae, Limeaceae, Lophiocarpaceae, Montiaceae and Talinaceae (all Caryophyllales) and Linderniaceae and Thomandersiaceae (both Lamiales). Use of bracketed families is abandoned because of its unpopularity, and in most cases the broader circumscriptions are retained; these include Amaryllidaceae, Asparagaceace and Xanthorrheaceae (all Asparagales), Passifloraceae (Malpighiales), Primulaceae (Ericales) and several other smaller families. Separate papers in this same volume deal with a new linear order for APG, subfamilial names that can be used for more accurate communication in Amaryllidaceae s.l., Asparagaceace s.l. and Xanthorrheaceae s.l. (all Asparagales) and a formal supraordinal classification for the flowering plants.", url = "https://doi.org/10.1111/j.1095-8339.2009.00996.x", doi = "10.1111/j.1095-8339.2009.00996.x", openalex = "W4245471709", references = "doi101046j109583392003t01100158x, doi101073pnas0708072104, doi101073pnas0709121104, doi101073pnas0813376106, doi101111j175348871981tb06752x, doi1023072484473, doi1023072992015, doi103732ajb0800047, doi103732ajb891132, doi105860choice453190, openalexw2961549061" } @article{doi101111j14610248200901410x, author = "Brodribb, Timothy J. and Feild, Taylor S.", title = "Leaf hydraulic evolution led a surge in leaf photosynthetic capacity during early angiosperm diversification", year = "2009", journal = "Ecology Letters", abstract = "Angiosperm evolution transformed global ecology, and much of this impact derives from the unrivalled vegetative productivity of dominant angiosperm clades. However, the origins of high photosynthetic capacity in angiosperms remain unknown. In this study, we describe the steep trajectory of leaf vein density (D(v)) evolution in angiosperms, and predict that this leaf plumbing innovation enabled a major shift in the capacity of leaves to assimilate CO(2). Reconstructing leaf vein evolution from an examination of 504 angiosperm species we found a rapid three- to fourfold increase in D(v) occurred during the early evolution of angiosperms. We demonstrate how this major shift in leaf vein architecture potentially allowed the maximum photosynthetic capacity in angiosperms to rise above competing groups 140-100 Ma. Our data suggest that early terrestrial angiosperms produced leaves with low photosynthetic rates, but that subsequent angiosperm success is linked to a surge in photosynthetic capacity during their early diversification.", url = "https://doi.org/10.1111/j.1461-0248.2009.01410.x", doi = "10.1111/j.1461-0248.2009.01410.x", openalex = "W2153946082", references = "doi101038282424a0, doi101046j14698137200200397x, doi101073pnas0709121104, doi101098rspb20081919, doi101111j14698137200400974x, doi101126science1155121, doi101126science2815374237, doi1023071218350, doi102475ajs294156, doi102475ajs3012182, doi103732ajb0800047, doi104159harvard9780674864856" } @article{doi103732ajb0800079, author = "Soltis, Pamela S. and Albert, Victor A. and Leebens‐Mack, Jim and Bell, Charles D. and Paterson, Andrew H. and Zheng, Chunfang and Sankoff, David and de Pamphilis, Claude W. and Wall, P. Kerr and Soltis, Pamela S.", title = "Polyploidy and angiosperm diversification", year = "2009", journal = "American Journal of Botany", abstract = {Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.}, url = "https://doi.org/10.3732/ajb.0800079", doi = "10.3732/ajb.0800079", openalex = "W2064911343", references = "doi101016jpalaeo200507006, doi101111j001438202001tb00826x, doi101146annurevgenet341401, doi101196annals1438005" } @article{doi1034172009143, author = "Boyce, C. Kevin and Lee, Jung‐Eun and Feild, Taylor S. and Brodribb, Timothy J. and Zwieniecki, Maciej A.", title = "Angiosperms Helped Put the Rain in the Rainforests: The Impact of Plant Physiological Evolution on Tropical Biodiversity 1", year = "2010", journal = "Annals of the Missouri Botanical Garden", abstract = "The recycling of transpired water is well known to be an important source of rainfall, particularly in the tropics, and angiosperms have transpiration capacities higher than any other plants throughout evolutionary history. Thus, the evolution and rise to ecological dominance of flowering plants are proposed to have strongly altered climate. Transpiration capacity is closely correlated with leaf vein density, and the average vein density of angiosperm leaves is four times greater than that of all other plants, living or extinct. A rapid transition to high vein densities occurred separately in three or more flowering plant lineages about 100 million years ago. Climate modeling of the impact of this physiological revolution indicates that the tropics would be hotter, drier, and more seasonal in the absence of the angiosperms, and the overall area of tropical rainforest would decline substantially. Because angiosperm diversity is influenced by rainforest area and by precipitation abundance and evenness, the high diversity of angiosperms is partially a product of a positive feedback loop with the climate modifications initiated by the angiosperms themselves. Lineage diversifications among vertebrate and invertebrate animals and nonangiospermous plants in the wake of the angiosperm radiation may be tied to the unprecedented impact of angiosperms on climate.", url = "https://doi.org/10.3417/2009143", doi = "10.3417/2009143", openalex = "W2100361465", references = "doi101038nature05634, doi101073pnas0608361104, doi101086282687, doi101111j1469185x1977tb01347x, doi101126science1066854, doi101126science1100217, doi101126science1164033, doi101126science1177265, doi1023073071998, doi102475ajs294156" } @incollection{crossref2011angiosperms, title = "Angiosperms", year = "2011", booktitle = "A Text-Book of Botany", url = "https://doi.org/10.1017/cbo9781139105231.012", doi = "10.1017/cbo9781139105231.012", pages = "466-586" } @article{doi101071fp11057, author = "Nicotra, Adrienne B. and Leigh, Andrea and Boyce, C. Kevin and Jones, Cynthia S. and Niklas, Karl J. and Royer, Dana L. and Tsukaya, Hirokazu", title = "The evolution and functional significance of leaf shape in the angiosperms", year = "2011", journal = "Functional Plant Biology", abstract = "Angiosperm leaves manifest a remarkable diversity of shapes that range from developmental sequences within a shoot and within crown response to microenvironment to variation among species within and between communities and among orders or families. It is generally assumed that because photosynthetic leaves are critical to plant growth and survival, variation in their shape reflects natural selection operating on function. Several non-mutually exclusive theories have been proposed to explain leaf shape diversity. These include: thermoregulation of leaves especially in arid and hot environments, hydraulic constraints, patterns of leaf expansion in deciduous species, biomechanical constraints, adaptations to avoid herbivory, adaptations to optimise light interception and even that leaf shape variation is a response to selection on flower form. However, the relative importance, or likelihood, of each of these factors is unclear. Here we review the evolutionary context of leaf shape diversification, discuss the proximal mechanisms that generate the diversity in extant systems, and consider the evidence for each the above hypotheses in the context of the functional significance of leaf shape. The synthesis of these broad ranging areas helps to identify points of conceptual convergence for ongoing discussion and integrated directions for future research.", url = "https://doi.org/10.1071/fp11057", doi = "10.1071/fp11057", openalex = "W2144704825", references = "doi101098rspb20081919, doi101104pp107101352, doi101111j14610248200901410x" } @article{doi101093aobmcr277, author = "te Beest, Mariska and Roux, Johannes J. Le and Richardson, David M. and Brysting, Anne K. and Suda, Jan and Kubešová, Magdalena and Pyšek, Petr", title = "The more the better? The role of polyploidy in facilitating plant invasions", year = "2011", journal = "Annals of Botany", abstract = "Polyploidy can be an important factor in species invasion success through a combination of (1) 'pre-adaptation', whereby polyploid lineages are predisposed to conditions in the new range and, therefore, have higher survival rates and fitness in the earliest establishment phase; and (2) the possibility for subsequent adaptation due to a larger genetic diversity that may assist the 'evolution of invasiveness'. Alternatively, polyploidization may play an important role by (3) restoring sexual reproduction following hybridization or, conversely, (4) asexual reproduction in the absence of suitable mates. We, therefore, encourage invasion biologists to incorporate assessments of ploidy in their studies of invasive alien species.", url = "https://doi.org/10.1093/aob/mcr277", doi = "10.1093/aob/mcr277", openalex = "W2061325948", references = "doi101016jtplants200912003, doi101038nrg1711, doi101038nrg2600, doi101073pnas0900906106, doi101111j10958339200900996x, doi101111j13669516200600302x, doi1011910309133306pp490pr" } @article{doi101111j13652486201102451x, author = "Kattge, Jens and Dı́az, Soledad and Lavorel, Sandra and Prentice, I. Colin and Leadley, Paul and Bönisch, Gerhard and Garnier, Éric and Westoby, Mark and Reich, Peter B. and Wright, Ian J. and Cornelissen, J. H. C. and Violle, Cyrille and Harrison, Sandy P. and van Bodegom, Peter M. and Reichstein, Markus and Enquist, Brian J. and Soudzilovskaia, Nadejda A. and Ackerly, David D. and Anand, M. and Atkin, Owen K. and Bahn, Michael and Baker, Timothy R. and Baldocchi, Dennis and Bekker, R.M. and Blanco, C. and Blonder, Benjamin and Bond, William J. and Bradstock, Ross A. and Bunker, Dan and Casanoves, Fernando and Cavender‐Bares, Jeannine and Chambers, Jeffrey Q. and Chapin, F. Stuart and Chave, Jérôme and Coomes, David A. and Cornwell, William K. and Craine, Joseph M. and Dobrin, Barbara and Duarte, Leandro and Durka, Walter and Elser, James J. and Esser, G. and Estiarte, Marc and Fagan, William F. and Fang, Jinwei and Fernández‐Méndez, Fernando and Fidélis, Alessandra and Finegan, Bryan and Flores, Olivier and FORD, HENRY and Frank, Dorothea and Freschet, Grégoire T. and Fyllas, Nikolaos M. and Gallagher, Rachael V. and GREEN, W. A. and Gutiérrez, Álvaro G. and Hickler, Thomas and Higgins, Steven I. and Hodgson, J. G. and Jalili, Amir and Jansen, Steven and Joly, Carlos Alfredo and Kerkhoff, Andrew J. and Kirkup, Donald W. and Kitajima, Kaoru and Kleyer, Michael and Klotz, Stefan and Knops, Johannes M. H. and Krämer, K. and Kühn, Ingolf and Kurokawa, H. and Laughlin, Daniel C. and Lee, Tali D. and Leishman, Michelle R. and Lens, Frederic and Lenz, Tanja I. and Lewis, Simon L. and Lloyd, Jon and Llusià, Joan and Louault, Frédérique and Ma, Sai and Mahecha, Miguel D. and Manning, Peter and Massad, Tara Joy and Medlyn, Belinda E. and Messier, J. and Moles, Angela T. and Müller, Sandra Cristina and Nadrowski, Karin and NAEEM, S. and Niinemets, Ülo and Nöllert, Stephanie and Nuske, Alison and Ogaya, Romà and Oleksyn, Jacek and Onipchenko, V. G. and Onoda, Yusuke and Ordóñez, Jenny and Overbeck, Gerhard E. and Ozinga, W.A.", title = "TRY – a global database of plant traits", year = "2011", journal = "Global Change Biology", abstract = "Abstract Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy‐in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log‐normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40\% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75\% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait‐based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.", url = "https://doi.org/10.1111/j.1365-2486.2011.02451.x", doi = "10.1111/j.1365-2486.2011.02451.x", openalex = "W2162584119", references = "doi101007bf00386231, doi1010160165176580900245, doi101016jtree200602002, doi101023a1004327224729, doi101038nature02403, doi101046j13652435200200664x, doi101046j13652486200300569x, doi101071bt02124, doi101086283244, doi101111j00301299200715559x, doi101111j14610248200600924x, doi101111j14610248200801219x, doi101146annurevecolsys33010802150452, doi1011552009421425" } @article{doi103732ajb1000404, author = "Soltis, Pamela S. and Smith, Stephen A. and Cellinese, Nico and Wurdack, Kenneth J. and Tank, David C. and Brockington, Samuel F. and Refulio, Nancy and Walker, Jay B. and Moore, Michael J. and Carlsward, Barbara S. and Bell, Charles D. and Latvis, Maribeth and Crawley, Sunny and Black, Chelsea M. and Diouf, Diaga and Xi, Zhenxiang and Rushworth, Catherine A. and Gitzendanner, Matthew A. and Sytsma, Kenneth J. and Qiu, Yin‐Long and Hilu, Khidir W. and Davis, Charles C. and Sanderson, Michael J. and Beaman, Reed S. and Olmstead, Richard G. and Judd, Walter S. and Donoghue, Michael J. and Soltis, Pamela S.", title = "Angiosperm phylogeny: 17 genes, 640 taxa", year = "2011", journal = "American Journal of Botany", abstract = "Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.", url = "https://doi.org/10.3732/ajb.1000404", doi = "10.3732/ajb.1000404", openalex = "W2123023543", references = "doi101016jympev200802011" } @article{doi101071bt12225, author = "Harguindeguy, Natalia Pérez and Dı́az, Sandra and Garnier, Éric and Lavorel, Sandra and Poorter, Hendrik and Jaureguiberry, Pedro and Bret‐Harte, M. Syndonia and Cornwell, William K. and Craine, Joseph M. and Gurvich, Diego E. and Urcelay, Carlos and Veneklaas, Erik J. and Reich, Peter B. and Poorter, Lourens and Wright, Ian J. and Ray, Peter M. and Enrico, Lucas and Pausas, Juli G. and de Vos, Arjen C. and Buchmann, Nina and Funes, Guillermo and Quétier, Fabien and Hodgson, John and Thompson, K. and Morgan, Huw D. and ter Steege, Hans and van der Heijden, Marcel G. A. and Sack, Lawren and Blonder, B. and Poschlod, Peter and Vaieretti, María V. and Conti, Georgina and Staver, A. Carla and Aquino, Sâmia and Cornelissen, J. H. C.", title = "New handbook for standardised measurement of plant functional traits worldwide", year = "2013", journal = "Australian Journal of Botany", abstract = "Plant functional traits are the features (morphological, physiological, phenological) that represent ecological strategies and determine how plants respond to environmental factors, affect other trophic levels and influence ecosystem properties. Variation in plant functional traits, and trait syndromes, has proven useful for tackling many important ecological questions at a range of scales, giving rise to a demand for standardised ways to measure ecologically meaningful plant traits. This line of research has been among the most fruitful avenues for understanding ecological and evolutionary patterns and processes. It also has the potential both to build a predictive set of local, regional and global relationships between plants and environment and to quantify a wide range of natural and human-driven processes, including changes in biodiversity, the impacts of species invasions, alterations in biogeochemical processes and vegetation–atmosphere interactions. The importance of these topics dictates the urgent need for more and better data, and increases the value of standardised protocols for quantifying trait variation of different species, in particular for traits with power to predict plant- and ecosystem-level processes, and for traits that can be measured relatively easily. Updated and expanded from the widely used previous version, this handbook retains the focus on clearly presented, widely applicable, step-by-step recipes, with a minimum of text on theory, and not only includes updated methods for the traits previously covered, but also introduces many new protocols for further traits. This new handbook has a better balance between whole-plant traits, leaf traits, root and stem traits and regenerative traits, and puts particular emphasis on traits important for predicting species’ effects on key ecosystem properties. We hope this new handbook becomes a standard companion in local and global efforts to learn about the responses and impacts of different plant species with respect to environmental changes in the present, past and future.", url = "https://doi.org/10.1071/bt12225", doi = "10.1071/bt12225", openalex = "W2101020813", references = "doi101006anbo20001261, doi101007s004420050100x, doi1010160031942281851345, doi101016b9780124735422x50007, doi101016jtree200602002, doi101023a1004327224729, doi10103835012241, doi101038nature02403, doi101038nature11148, doi101098rspb20081919, doi101104pp107101352, doi101111j00301299200715559x, doi101111j13652486201102451x, doi101111j14610248200801219x, doi101111j14610248200901285x, doi101111j14610248200901314x, doi101111j14610248200901410x, doi101146annurevecolsys33010802150452, doi101146annurevpp40060189002443, doi1023073241344, doi105860choice324498, openalexw1573494572, openalexw2058502945, openalexw2764433274, openalexw569951484" } @article{doi101093sysbiosyt034, author = "Beaulieu, Jeremy M. and O’Meara, Brian C. and Donoghue, Michael J.", title = "Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms", year = "2013", journal = "Systematic Biology", abstract = "The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.", url = "https://doi.org/10.1093/sysbio/syt034", doi = "10.1093/sysbio/syt034", openalex = "W2112282403", references = "doi101093bioinformaticsbtl446, doi101093bioinformaticsbtq706, doi101093nargkh340, doi101109tac19741100705, doi101111j10958339200900996x, doi1023071266136, doi1023072004114, doi1023073802723, openalexw2611511275, openalexw3149745985" } @article{doi101126science1241089, author = "Project, Amborella Genome and Albert, Victor A. and Barbazuk, W. Brad and dePamphilis, Claude W. and Der, Joshua P. and Leebens-Mack, James and Mā, Hong and Palmer, Jeffrey D. and Rounsley, Steve and Sankoff, David and Schuster, Stephan C. and Soltis, Pamela S. and Soltis, Pamela S. and Wessler, Susan R. and Wing, Rod A. and Albert, Victor A. and Ammiraju, Jetty S. S. and Barbazuk, W. Bradley and Chamala, Srikar and Chanderbali, Andre S. and dePamphilis, Claude W. and Der, Joshua P. and Determann, Ronald and Leebens-Mack, James and Ma, Hong and Ralph, Paula E. and Rounsley, Steve and Schuster, Stephan C. and Soltis, Douglas E. and Soltis, Pamela S. and Talag, Jason and Tomsho, Lynn and Walts, Brandon and Wanke, Stefan and Wing, Rod A. and Albert, Victor A. and Barbazuk, W. Brad and Chamala, Srikar and Chanderbali, Andre S. and Chang, Tien-Hao and Determann, Ronald and Lan, Tianying and Soltis, Douglas E. and Soltis, Pamela S. and Arikit, Siwaret and Axtell, Michael J. and Ayyampalayam, Saravanaraj and Barbazuk, W. Brad and Burnette, James M. and Chamala, Srikar and Paoli, Emanuele De and dePamphilis, Claude W. and Der, Joshua P. and Estill, James C. and Farrell, Nina and Harkess, Alex and Jiao, Yuannian and Leebens-Mack, James and Liu, Kun and Mei, Wenbin and Meyers, Blake C. and Shahid, Saima and Wafula, Eric and Walts, Brandon and Wessler, Susan R. and Zhai, Jixian and Zhang, Xiaoyu and Albert, Victor A. and Carretero-Paulet, Lorenzo and dePamphilis, Claude W. and Der, Joshua P. and Jiao, Yuannian and Leebens-Mack, James and Lyons, Eric and Sankoff, David and Tang, Haibao and Wafula, Eric and Zheng, Chunfang and Albert, Victor A. and Altman, Naomi S. and Barbazuk, W. Bradley and Carretero-Paulet, Lorenzo and dePamphilis, Claude W. and Der, Joshua P. and Estill, James C. and Jiao, Yuannian and Leebens-Mack, James and Liu, Kun and Mei, Wenbin and Wafula, Eric and Altman, Naomi S. and Arikit, Siwaret and Axtell, Michael J. and Chamala, Srikar and Chanderbali, Andre S. and Chen, Feng and Chen, Jian‐Qun and Chiang, Vincent L. and Paoli, Emanuele De and dePamphilis, Claude W.", title = "The Amborella Genome and the Evolution of Flowering Plants", year = "2013", journal = "Science", abstract = "Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.", url = "https://doi.org/10.1126/science.1241089", doi = "10.1126/science.1241089", openalex = "W2058378183", references = "doi101016jpalaeo200507006, doi101146annurevearth042711105313, doi101196annals1438005" } @misc{crossref2014angiosperms, title = "ANGIOSPERMS", year = "2014", booktitle = "Encyclopedia of Environmental Change", url = "https://doi.org/10.4135/9781446247501.n178", doi = "10.4135/9781446247501.n178" } @article{doi101038ncomms5087, author = "Werner, Gijsbert D. A. and Cornwell, William K. and Sprent, Janet I. and Kattge, Jens and Kiers, E. Toby", title = "A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms", year = "2014", journal = "Nature Communications", abstract = "Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis' evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of 'stable fixers' (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships.", url = "https://doi.org/10.1038/ncomms5087", doi = "10.1038/ncomms5087", openalex = "W2031705623", references = "doi101038nature10625, doi101038nature12872, doi101038nrmicro1987, doi101038nrmicro2990, doi101093bibbbn013, doi101093bioinformaticsbtl446, doi101093sysbiosyt034, doi101098rspb19940006, doi101111j13652486201102451x, doi101111j155856461985tb00420x, doi103758bf03206482" } @article{doi101073pnas1323926111, author = "Wickett, Norman J. and Mirarab, Siavash and Nguyen, Nam and Warnow, Tandy and Carpenter, Eric and Matasci, Naim and Ayyampalayam, Saravanaraj and Barker, Michael S. and Burleigh, J. Gordon and Gitzendanner, Matthew A. and Ruhfel, Brad R. and Wafula, Eric and Der, Joshua P. and Graham, Sean W. and Mathews, Sarah and Melkonian, Michael and Soltis, Pamela S. and Soltis, Pamela S. and Miles, Nicholas W. and Rothfels, Carl J. and Pokorny, Lisa and Shaw, A. Jonathan and DeGironimo, Lisa and Stevenson, Dennis and Surek, Barbara and Villarreal, Juan Carlos and Roure, Béatrice and Philippe, Hervé and dePamphilis, Claude W. and Chen, Tao and Deyholos, Michael K. and Baucom, Regina S. and Kutchan, Toni M. and Augustin, Megan M. and Wang, Jun and Zhang, Yong and Tian, Zhijian and Yan, Zhixiang and Wu, Xiaolei and Sun, Xiao and Wong, Gane Ka‐Shu and Leebens-Mack, James", title = "Phylotranscriptomic analysis of the origin and early diversification of land plants", year = "2014", journal = "Proceedings of the National Academy of Sciences", abstract = "Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.", url = "https://doi.org/10.1073/pnas.1323926111", doi = "10.1073/pnas.1323926111", openalex = "W2013277649", references = "doi101016jtree200901009, doi101016s0022283605803602, doi10103837918, doi101046j109583392003t01100158x, doi101093bioinformatics83275, doi101093bioinformaticsbtl446, doi101093sysbio463523, doi101093sysbiosyt022, doi101111boj12385, doi101111j10958339200900996x, doi101111j10960031200800217x, doi1011861471214811104, doi101371journalpcbi1002195, doi1023072346830, openalexw3148514506" } @article{doi101098rspb20132829, author = "Zwieniecki, Maciej A. and Boyce, C. Kevin", title = "Evolution of a unique anatomical precision in angiosperm leaf venation lifts constraints on vascular plant ecology", year = "2014", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "The main role of leaf venation is to supply water across the photosynthetic surface to keep stomata open and allow access to atmospheric CO2 despite evaporative demand. The optimal uniform delivery of water occurs when the distance between veins equals the depth of vein placement within the leaf away from the evaporative surface. As presented here, only angiosperms maintain this anatomical optimum across all leaf thicknesses and different habitats, including sheltered environments where this optimization need not be required. Intriguingly, basal angiosperm lineages tend to be underinvested hydraulically; uniformly high optimization is derived independently in the magnoliids, monocots and core eudicots. Gymnosperms and ferns, including available fossils, are limited by their inability to produce high vein densities. The common association of ferns with shaded humid environments may, in part, be a direct evolutionary consequence of their inability to produce hydraulically optimized leaves. Some gymnosperms do approach optimal vein placement, but only by virtue of their ability to produce thick leaves most appropriate in environments requiring water conservation. Thus, this simple anatomical metric presents an important perspective on the evolution and phylogenetic distribution of plant ecologies and further evidence that the vegetative biology of flowering plants-not just their reproductive biology-is unique.", url = "https://doi.org/10.1098/rspb.2013.2829", doi = "10.1098/rspb.2013.2829", openalex = "W2118988740", references = "doi101007b138533, doi101086300102, doi101098rspb20081919, doi101104pp107101352, doi101111j109583121989tb00492x, doi101111j14610248200901410x, doi1016660094837320040300082dadani20co2, doi1023073515620, openalexw2097450069" } @article{doi1011111365274512211, author = "Reich, Peter B.", title = "The world‐wide ‘fast–slow’ plant economics spectrum: a traits manifesto", year = "2014", journal = "Journal of Ecology", abstract = "Summary The leaf economics spectrum (LES) provides a useful framework for examining species strategies as shaped by their evolutionary history. However, that spectrum, as originally described, involved only two key resources (carbon and nutrients) and one of three economically important plant organs. Herein, I evaluate whether the economics spectrum idea can be broadly extended to water – the third key resource –stems, roots and entire plants and to individual, community and ecosystem scales. My overarching hypothesis is that strong selection along trait trade‐off axes, in tandem with biophysical constraints, results in convergence for any taxon on a uniformly fast, medium or slow strategy (i.e. rates of resource acquisition and processing) for all organs and all resources. Evidence for economic trait spectra exists for stems and roots as well as leaves, and for traits related to water as well as carbon and nutrients. These apply generally within and across scales (within and across communities, climate zones, biomes and lineages). There are linkages across organs and coupling among resources, resulting in an integrated whole‐plant economics spectrum. Species capable of moving water rapidly have low tissue density, short tissue life span and high rates of resource acquisition and flux at organ and individual scales. The reverse is true for species with the slow strategy. Different traits may be important in different conditions, but as being fast in one respect generally requires being fast in others, being fast or slow is a general feature of species. Economic traits influence performance and fitness consistent with trait‐based theory about underlying adaptive mechanisms. Traits help explain differences in growth and survival across resource gradients and thus help explain the distribution of species and the assembly of communities across light, water and nutrient gradients. Traits scale up – fast traits are associated with faster rates of ecosystem processes such as decomposition or primary productivity, and slow traits with slow process rates. Synthesis. Traits matter. A single ‘fast–slow’ plant economics spectrum that integrates across leaves, stems and roots is a key feature of the plant universe and helps to explain individual ecological strategies, community assembly processes and the functioning of ecosystems.", url = "https://doi.org/10.1111/1365-2745.12211", doi = "10.1111/1365-2745.12211", openalex = "W2127928904", references = "doi101023a1004327224729, doi101038nature02403, doi101046j13652435200200664x, doi101046j13652745199800306x, doi101086283244, doi101098rspb20081919, doi101104pp107101352, doi101111j00301299200715559x, doi101111j109583121989tb00492x, doi101111j13652486201102451x, doi101111j14610248200801219x, doi101111j14610248200901285x, doi101111j14610248200901314x, doi101111j14610248200901410x, doi101146annureves11110180001313, doi1018900012965819970781958cafasa20co2, doi1023072259756, doi1023074549, doi1034172009143, openalexw1564371012, openalexw2097450069, openalexw2169917233" } @article{doi101111nph12782, author = "Willis, Charles G. and Baskin, Carol C. and Baskin, Jerry M. and Auld, Josh R. and Venable, D. Lawrence and Cavender‐Bares, Jeannine and Donohue, Kathleen and de Casas, Rafael Rubio and Group, The NESCent Germination Working", title = "The evolution of seed dormancy: environmental cues, evolutionary hubs, and diversification of the seed plants", year = "2014", journal = "New Phytologist", abstract = "Seed dormancy, by controlling the timing of germination, can strongly affect plant survival. The kind of seed dormancy, therefore, can influence both population and species-level processes such as colonization, adaptation, speciation, and extinction. We used a dataset comprising over 14,000 taxa in 318 families across the seed plants to test hypotheses on the evolution of different kinds of seed dormancy and their association with lineage diversification. We found morphophysiological dormancy to be the most likely ancestral state of seed plants, suggesting that physiologically regulated dormancy in response to environmental cues was present at the origin of seed plants. Additionally, we found that physiological dormancy (PD), once disassociated from morphological dormancy, acted as an 'evolutionary hub' from which other dormancy classes evolved, and that it was associated with higher rates of lineage diversification via higher speciation rates. The environmental sensitivity provided by dormancy in general, and by PD in particular, appears to be a key trait in the diversification of seed plants.", url = "https://doi.org/10.1111/nph.12782", doi = "10.1111/nph.12782", openalex = "W2110336319", references = "doi101111j001438202002tb00137x, doi10118614712105788" } @article{doi101146annurevecolsys120213091905, author = "Donoghue, Michael J. and Edwards, Erika J.", title = "Biome Shifts and Niche Evolution in Plants", year = "2014", journal = "Annual Review of Ecology Evolution and Systematics", abstract = "What factors influence whether a lineage can successfully transition into a new biome, and why have some biome shifts been more frequent than others? To orient this line of research we develop a conceptual framework in which the likelihood of a biome shift is a function of (a) exposure to contrasting environments over time, (b) the evolutionary accessibility of relevant adaptations, and (c) changing biotic interactions. We evaluate the literature on biome shifts in plants in relation to a set of hypotheses on the size, connectedness, and absolute age of biomes, as well as on the adaptability of particular lineages and ecological interactions over time. We also critique the phylogenetic inference of past biomes and a “global” model-based approach to biome evolution. More robust generalizations about biome shifts will require detailed studies of well-sampled and well-resolved clades, accounting for changes in the relevant abiotic and biotic factors through time.", url = "https://doi.org/10.1146/annurev-ecolsys-120213-091905", doi = "10.1146/annurev-ecolsys-120213-091905", openalex = "W2141294262", references = "doi101002joc1276, doi101016jtplants201009008, doi101016jtree200409011, doi101038nature12872, doi101093oso97801951223430010001, doi101093sysbiosyt034, doi101111j14610248200801229x, doi101111j14610248201001515x, doi101146annurevecolsys36102803095431, doi1016410006356820010510933teotwa20co2, openalexw2273605253" } @article{doi101086682022, author = "Pennell, Matthew W. and FitzJohn, Richard G. and Cornwell, William K. and Harmon, Luke J.", title = "Model Adequacy and the Macroevolution of Angiosperm Functional Traits", year = "2015", journal = "The American Naturalist", abstract = "Making meaningful inferences from phylogenetic comparative data requires a meaningful model of trait evolution. It is thus important to determine whether the model is appropriate for the data and the question being addressed. One way to assess this is to ask whether the model provides a good statistical explanation for the variation in the data. To date, researchers have focused primarily on the explanatory power of a model relative to alternative models. Methods have been developed to assess the adequacy, or absolute explanatory power, of phylogenetic trait models, but these have been restricted to specific models or questions. Here we present a general statistical framework for assessing the adequacy of phylogenetic trait models. We use our approach to evaluate the statistical performance of commonly used trait models on 337 comparative data sets covering three key angiosperm functional traits. In general, the models we tested often provided poor statistical explanations for the evolution of these traits. This was true for many different groups and at many different scales. Whether such statistical inadequacy will qualitatively alter inferences drawn from comparative data sets will depend on the context. Regardless, assessing model adequacy can provide interesting biological insights-how and why a model fails to describe variation in a data set give us clues about what evolutionary processes may have driven trait evolution across time.", url = "https://doi.org/10.1086/682022", doi = "10.1086/682022", openalex = "W2952286239", references = "doi101146annurevecolsys120213091905" } @article{doi101111nph13491, author = "Tank, David C. and Eastman, Jonathan M. and Pennell, Matthew W. and Soltis, Pamela S. and Soltis, Pamela S. and Hinchliff, Cody E. and Brown, Joseph W. and Sessa, Emily B. and Harmon, Luke J.", title = "Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications", year = "2015", journal = "New Phytologist", abstract = "Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity. Using a time-calibrated phylogeny, we characterized hot and cold spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also tested the whole-genome duplication (WGD) radiation lag-time model, which postulates that increases in diversification tend to lag behind established WGD events. Diversification rates have been incredibly heterogeneous throughout the evolutionary history of angiosperms and reveal a pattern of 'nested radiations' - increases in net diversification nested within other radiations. This pattern in turn generates a negative relationship between clade age and diversity across both families and orders. We suggest that stochastically changing diversification rates across the phylogeny explain these patterns. Finally, we demonstrate significant statistical support for the WGD radiation lag-time model. Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time. These diversification shifts are only rarely perfectly associated with WGD events, but commonly follow them after a lag period.", url = "https://doi.org/10.1111/nph.13491", doi = "10.1111/nph.13491", openalex = "W2159372152", references = "doi101111j14610248200901410x, doi101111j14754983201001011x" } @article{doi101071bt12225co, author = "Harguindeguy, Natalia Pérez and Díaz, Silvia and Garnier, Éric and Lavorel, Sandra and Poorter, Hendrik and Jaureguiberry, Pedro and Bret‐Harte, M. Syndonia and Cornwell, William K. and Craine, Joseph M. and Gurvich, Diego E. and Urcelay, Carlos and Veneklaas, Erik J. and Reich, Peter B. and Poorter, Lourens and Wright, Ian J. and Ray, Prasun and Enrico, Lucas and Pausas, Juli G. and Vos, Ad and Buchmann, Nina and Funes, Guillermo and Quétier, Fabien and Hodgson, John and Thompson, Ken and Morgan, Huw D. and ter Steege, Hans and Sack, Lawren and Blonder, B. and Poschlod, Peter and Vaieretti, María V. and Conti, Georgina and Staver, A. Carla and Aquino, Sâmia and Cornelissen, J. H. C.", title = "Corrigendum to: New handbook for standardised measurement of plant functional traits worldwide", year = "2016", journal = "Australian Journal of Botany", abstract = "Plant functional traits are the features (morphological, physiological, phenological) that represent ecological strategies and determine how plants respond to environmental factors, affect other trophic levels and influence ecosystem properties. Variation in plant functional traits, and trait syndromes, has proven useful for tackling many important ecological questions at a range of scales, giving rise to a demand for standardised ways to measure ecologically meaningful plant traits. This line of research has been among the most fruitful avenues for understanding ecological and evolutionary patterns and processes. It also has the potential both to build a predictive set of local, regional and global relationships between plants and environment and to quantify a wide range of natural and human-driven processes, including changes in biodiversity, the impacts of species invasions, alterations in biogeochemical processes and vegetation–atmosphere interactions. The importance of these topics dictates the urgent need for more and better data, and increases the value of standardised protocols for quantifying trait variation of different species, in particular for traits with power to predict plant- and ecosystem-level processes, and for traits that can be measured relatively easily. Updated and expanded from the widely used previous version, this handbook retains the focus on clearly presented, widely applicable, step-by-step recipes, with a minimum of text on theory, and not only includes updated methods for the traits previously covered, but also introduces many new protocols for further traits. This new handbook has a better balance between whole-plant traits, leaf traits, root and stem traits and regenerative traits, and puts particular emphasis on traits important for predicting species' effects on key ecosystem properties. We hope this new handbook becomes a standard companion in local and global efforts to learn about the responses and impacts of different plant species with respect to environmental changes in the present, past and future.", url = "https://doi.org/10.1071/bt12225\_co", doi = "10.1071/bt12225\_co", openalex = "W2561479186", references = "doi101006anbo20001261, doi101098rspb20081919, doi101104pp107101352, doi101111j14610248200901410x" } @article{doi101111boj12385, author = "Group, The Angiosperm Phylogeny", title = "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV", year = "2016", journal = "Botanical Journal of the Linnean Society", abstract = "© 2016 The Linnean Society of London. An update of the Angiosperm Phylogeny Group (APG) classification of the orders and families of angiosperms is presented. Several new orders are recognized: Boraginales, Dilleniales, Icacinales, Metteniusiales and Vahliales. This brings the total number of orders and families recognized in the APG system to 64 and 416, respectively. We propose two additional informal major clades, superrosids and superasterids, that each comprise the additional orders that are included in the larger clades dominated by the rosids and asterids. Families that made up potentially monofamilial orders, Dasypogonaceae and Sabiaceae, are instead referred to Arecales and Proteales, respectively. Two parasitic families formerly of uncertain positions are now placed: Cynomoriaceae in Saxifragales and Apodanthaceae in Cucurbitales. Although there is evidence that some families recognized in APG III are not monophyletic, we make no changes in Dioscoreales and Santalales relative to APG III and leave some genera in Lamiales unplaced (e.g. Peltanthera). These changes in familial circumscription and recognition have all resulted from new results published since APG III, except for some changes simply due to nomenclatural issues, which include substituting Asphodelaceae for Xanthorrhoeaceae (Asparagales) and Francoaceae for Melianthaceae (Geraniales); however, in Francoaceae we also include Bersamaceae, Ledocarpaceae, Rhynchothecaceae and Vivianiaceae. Other changes to family limits are not drastic or numerous and are mostly focused on some members of the lamiids, especially the former Icacinaceae that have long been problematic with several genera moved to the formerly monogeneric Metteniusaceae, but minor changes in circumscription include Aristolochiaceae (now including Lactoridaceae and Hydnoraceae; Aristolochiales), Maundiaceae (removed from Juncaginaceae; Alismatales), Restionaceae (now re-including Anarthriaceae and Centrolepidaceae; Poales), Buxaceae (now including Haptanthaceae; Buxales), Peraceae (split from Euphorbiaceae; Malpighiales), recognition of Petenaeaceae (Huerteales), Kewaceae, Limeaceae, Macarthuriaceae and Microteaceae (all Caryophyllales), Petiveriaceae split from Phytolaccaceae (Caryophyllales), changes to the generic composition of Ixonanthaceae and Irvingiaceae (with transfer of Allantospermum from the former to the latter; Malpighiales), transfer of Pakaraimaea (formerly Dipterocarpaceae) to Cistaceae (Malvales), transfer of Borthwickia, Forchhammeria, Stixis and Tirania (formerly all Capparaceae) to Resedaceae (Brassicales), Nyssaceae split from Cornaceae (Cornales), Pteleocarpa moved to Gelsemiaceae (Gentianales), changes to the generic composition of Gesneriaceae (Sanango moved from Loganiaceae) and Orobanchaceae (now including Lindenbergiaceae and Rehmanniaceae) and recognition of Mazaceae distinct from Phrymaceae (all Lamiales).", url = "https://doi.org/10.1111/boj.12385", doi = "10.1111/boj.12385", openalex = "W2166152751", references = "doi1010079783642143977, doi101046j109583392003t01100158x, doi101073pnas1323926111, doi101111j10958339200900996x, doi101111j109600311996tb00196x, doi101111j155856461985tb00420x, doi1023071222465, doi1023072399846, doi10230725065646, doi103732ajb0800047, openalexw3148514506, openalexw70084438" } @article{doi101038ncomms16047, author = "Sauquet, Hervé and von Balthazar, Maria and Magallón, Susana and Doyle, James A. and Endress, Peter K. and Bailes, Emily J. and de Morais, Érica Barroso and Bull–Hereñu, Kester and Carrive, Laetitia and Chartier, Marion and Chomicki, Guillaume and Coiro, Mario and Cornette, Raphaël and Ottra, Juliana Hanna Leite El and Epicoco, Cyril and Foster, Charles S. P. and Jabbour, Florian and Haevermans, Agathe and Haevermans, Thomas and Hernández, Rebeca and Little, Stefan A. and Löfstrand, Stefan and Luna, Javier A. and Massoni, Julien and Nadot, Sophie and Pamperl, Susanne and Prieu, Charlotte and Reyes, Elisabeth and dos Santos, Patrícia and Schoonderwoerd, Kristel M. and Sontag, Susanne and Soulebeau, Anaëlle and Staedler, Yannick M. and Tschan, Georg F. and Leung, Amy Wing-Sze and Schönenberger, Jürg", title = "The ancestral flower of angiosperms and its early diversification", year = "2017", journal = "Nature Communications", abstract = "Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms.", url = "https://doi.org/10.1038/ncomms16047", doi = "10.1038/ncomms16047", openalex = "W2741748285", references = "doi101073pnas0709121104, doi101073pnas1323926111, doi101080106351501753462876, doi10108010635150490522232, doi10108010635150490522304, doi10108010635150701607033, doi101086675935, doi101093bioinformaticsbtq706, doi101093molbevmss075, doi101093sysbiosyt034, doi101098rspb19940006, doi1011112041210x12420, doi101111boj12385, doi101146annurevearth042711105313, doi103732ajb0800047" } @article{doi101093aobmcx079, author = "Alix, Karine and Gérard, P. and Schwarzacher, Trude and Heslop‐Harrison, J. S.", title = "Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants", year = "2017", journal = "Annals of Botany", abstract = "The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.", url = "https://doi.org/10.1093/aob/mcx079", doi = "10.1093/aob/mcx079", openalex = "W2734942911", references = "doi101002bies201100035, doi101016jpalaeo200507006, doi101111j14697998201100829x" } @article{doi101126scienceaad4501, author = "Martin, Francis and Uroz, Stéphane and Barker, David G.", title = "Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria", year = "2017", journal = "Science", abstract = "Within the plant microbiota, mutualistic fungal and bacterial symbionts are striking examples of microorganisms playing crucial roles in nutrient acquisition. They have coevolved with their hosts since initial plant adaptation to land. Despite the evolutionary distances that separate mycorrhizal and nitrogen-fixing symbioses, these associations share a number of highly conserved features, including specific plant symbiotic signaling pathways, root colonization strategies that circumvent plant immune responses, functional host-microbe interface formation, and the central role of phytohormones in symbiosis-associated root developmental pathways. We highlight recent and emerging areas of investigation relating to these evolutionarily conserved mechanisms, with an emphasis on the more ancestral mycorrhizal associations, and consider to what extent this knowledge can contribute to an understanding of plant-microbiota associations as a whole.", url = "https://doi.org/10.1126/science.aad4501", doi = "10.1126/science.aad4501", openalex = "W2618012128", references = "doi101038ncomms5087, doi101098rstb20110271" } @article{doi101146annurevearth063016015629, author = "Boyce, C. Kevin and Lee, Jung‐Eun", title = "Plant Evolution and Climate Over Geological Timescales", year = "2017", journal = "Annual Review of Earth and Planetary Sciences", abstract = "The terrestrial vegetation is unambiguously an important factor in the climate system, modulating the exchange of energy, momentum, water vapor, and other trace gases between land and atmosphere. Here, we review the evolution of the terrestrial flora from the Proterozoic through to the Neogene at three distinct scales—the overall evolution of floral composition, the evolution of plant physiology, and the evolution of landscape occupation both spatially and seasonally—all in the context of how the vegetation may have influenced climate through time and which deep-time evolutionary transitions may have had the greatest effect. Our focus is upon the direct impacts of the vegetation on temperature and precipitation, but we also consider the indirect impacts of plants on climate via atmospheric composition. We argue that the times of greatest change in plant climate feedbacks are likely to have been the Carboniferous and the early Paleogene.", url = "https://doi.org/10.1146/annurev-earth-063016-015629", doi = "10.1146/annurev-earth-063016-015629", openalex = "W2523635891", references = "doi101098rspb20132829, doi101126science1260947" } @article{doi101002ajb21019, author = "Smith, Stephen A. and Brown, Joseph W.", title = "Constructing a broadly inclusive seed plant phylogeny", year = "2018", journal = "American Journal of Botany", abstract = "This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.", url = "https://doi.org/10.1002/ajb2.1019", doi = "10.1002/ajb2.1019", openalex = "W2792688220", references = "doi101038nature11631, doi101038nature12872, doi101038ncomms16047, doi101038ncomms2958, doi101073pnas1323926111, doi101093oxfordjournalsmolbeva003974, doi101111nph13264, doi101111syen12037" } @article{doi101098rspb20181012, author = "Ran, Jin‐Hua and Shen, Tingting and Wang, Mingming and Wang, Xiaoquan", title = "Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms", year = "2018", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylogenetic conflict, we conducted a phylotranscriptomic study with a sampling of all 13 families of gymnosperms and main lineages of angiosperms. Multiple datasets containing up to 1 296 042 sites across 1308 loci were analysed, using concatenation and coalescence approaches. Our study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis. Cycads plus Ginkgo is sister to the remaining gymnosperms. We also found that Gnetales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms. This implies that Gnetales and angiosperms might have experienced similar selective pressures in evolutionary histories. Convergent molecular evolution or homoplasy is partially responsible for the phylogenetic conflicts in seed plants. Our study provides a robustly reconstructed backbone phylogeny that is important for future molecular and morphological studies of seed plants, in particular gymnosperms, in the light of evolution.", url = "https://doi.org/10.1098/rspb.2018.1012", doi = "10.1098/rspb.2018.1012", openalex = "W2808886394", references = "doi101038nbt1883, doi101038nprot2013084, doi101093bioinformaticsbtl158, doi101093bioinformaticsbtu033, doi101093bioinformaticsbtu170, doi101093molbevmsm088, doi101093molbevmst010, doi101093molbevmsw260, doi101093sysbiosys029, doi101186s1305901507212" } @article{doi101111nph14976, author = "Brundrett, Mark and Tedersoo, Leho", title = "Evolutionary history of mycorrhizal symbioses and global host plant diversity", year = "2018", journal = "New Phytologist", abstract = "Contents Summary 1108 I. Introduction 1108 II. Mycorrhizal plant diversity at global and local scales 1108 III. Mycorrhizal evolution in plants: a brief update 1111 IV. Conclusions and perspectives 1114 References 1114 SUMMARY: The majority of vascular plants are mycorrhizal: 72\% are arbuscular mycorrhizal (AM), 2.0\% are ectomycorrhizal (EcM), 1.5\% are ericoid mycorrhizal and 10\% are orchid mycorrhizal. Just 8\% are completely nonmycorrhizal (NM), whereas 7\% have inconsistent NM-AM associations. Most NM and NM-AM plants are nutritional specialists (e.g. carnivores and parasites) or habitat specialists (e.g. hydrophytes and epiphytes). Mycorrhizal associations are consistent in most families, but there are exceptions with complex roots (e.g. both EcM and AM). We recognize three waves of mycorrhizal evolution, starting with AM in early land plants, continuing in the Cretaceous with multiple new NM or EcM linages, ericoid and orchid mycorrhizas. The third wave, which is recent and ongoing, has resulted in root complexity linked to rapid plant diversification in biodiversity hotspots.", url = "https://doi.org/10.1111/nph.14976", doi = "10.1111/nph.14976", openalex = "W2792482912", references = "doi101038nature12872, doi101038ncomms5087, doi101038nrg201726, doi101146annurevearth261379" } @article{doi101111nph15572, author = "Deans, Ross M. and Brodribb, Timothy J. and Busch, Florian A. and Farquhar, Graham D.", title = "Plant water‐use strategy mediates stomatal effects on the light induction of photosynthesis", year = "2018", journal = "New Phytologist", abstract = "More efficient gas exchange strategies under dynamic light environments have been hypothesised to contribute to the dominance of angiosperms in the vascular plant flora. However, we still lack a clear understanding of how stomatal dynamics affect photosynthetic dynamics and whether differences exist between lineages. Stomatal and photosynthetic dynamics following changes in irradiance were studied in 15 species, encompassing ferns, gymnosperms and angiosperms. We determined the effect of stomatal speed on dynamic photosynthesis and water loss. Moreover, we assessed whether dynamic behaviour followed evolutionary lineage divisions, or whether ecological adaptation to maximise light fleck use could describe dynamic behaviour. We found that species with fast stomatal opening, such as ferns, forgo less photosynthesis during photosynthetic induction. By contrast, there was no relationship between stomatal closure speed and the water wasted by transiently more-open stomata, because species with higher rates of gas exchange also showed faster stomatal closure. Shade-adapted species possessed fast-opening but slow-closing stomata, consistent with ecological adaptation to maximise light fleck use. Our results suggest dynamic behaviour follows adaptive ecological trends more strongly than evolutionary ones, but angiosperms may benefit from relatively faster photosynthetic induction by adopting a less conservative water-use strategy.", url = "https://doi.org/10.1111/nph.15572", doi = "10.1111/nph.15572", openalex = "W2899292980", references = "doi101098rspb20132829" } @incollection{crossref2019angiosperms, title = "Angiosperms", year = "2019", booktitle = "Introduction to Plant Fossils", url = "https://doi.org/10.1017/9781108650021.010", doi = "10.1017/9781108650021.010", pages = "188-212" } @article{doi101038s4158601918525, author = "Zhang, Liangsheng and Chen, Fei and Zhang, Xingtan and Li, Zhen and Zhao, Yiyong and Lohaus, Rolf and Chang, Xiaojun and Dong, Wei and Ho, Simon Y. W. and Liu, Xing and Song, Aixia and Chen, Junhao and Guo, Wenlei and Wang, Zhengjia and Zhuang, Yingyu and Wang, Haifeng and Chen, Xuequn and Hu, Juan and Liu, Yanhui and Qin, Yuan and Wang, Kai and Dong, Shanshan and Liu, Yang and Zhang, Shouzhou and Yu, Xianxian and Wu, Qian and Wang, Liangsheng and Yan, Xueqing and Jiao, Yuannian and Kong, Hongzhi and Zhou, Xiaofan and Yu, Cuiwei and Chen, Yuchu and Li, Fan and Wang, Jihua and Chen, Wei and Chen, Xinlu and Jia, Qidong and Zhang, Chi and Jiang, Yifan and Zhang, Wanbo and Liu, Guanhua and Fu, Jianyu and Chen, Feng and Mā, Hong and de Peer, Yves Van and Tang, Haibao", title = "The water lily genome and the early evolution of flowering plants", year = "2019", journal = "Nature", abstract = "Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms 1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.", url = "https://doi.org/10.1038/s41586-019-1852-5", doi = "10.1038/s41586-019-1852-5", openalex = "W2995259736", references = "doi101038ncomms16047, doi101111j14698137201103794x" } @article{doi101111brv12570, author = "Zanne, Amy E. and Abarenkov, Kessy and Afkhami, Michelle E. and Aguilar‐Trigueros, Carlos A. and Bates, Scott T. and Bhatnagar, Jennifer and Busby, Posy E. and Christian, Natalie and Cornwell, William K. and Crowther, Thomas W. and Flores‐Moreno, Habacuc and Floudas, Dimitrios and Gazis, Romina and Hibbett, David S. and Kennedy, Peter G. and Lindner, Daniel L. and Maynard, Daniel S. and Milo, Amy M. and Nilsson, Rolf Henrik and Powell, Jeff R. and Schildhauer, Mark and Schilling, Jonathan S. and Treseder, Kathleen K.", title = "Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi", year = "2019", journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society", abstract = "Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun Fun). Fun Fun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.", url = "https://doi.org/10.1111/brv.12570", doi = "10.1111/brv.12570", openalex = "W2991566198", references = "doi101093sysbiosyy031" } @article{doi101111ecog04434, author = "Jin, Yi and Qian, Hong", title = "V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants", year = "2019", journal = "Ecography", abstract = "We present V.PhyloMaker, a freely available package for R designed to generate phylogenies for vascular plants. The mega‐tree implemented in V.PhyloMaker (i.e. GBOTB.extended.tre), which was derived from two recently published mega‐trees and includes 74 533 species and all families of extant vascular plants, is the largest dated phylogeny for vascular plants. V.PhyloMaker can generate phylogenies for very large species lists (the largest species list that we tested included 314 686 species). V.PhyloMaker generates phylogenies at a fast speed, much faster than other phylogeny‐generating packages. Our tests of V.PhyloMaker show that generating a phylogeny for 60 000 species requires less than six hours. V.PhyloMaker includes an approach to attach genera or species to their close relatives in a phylogeny. We provide a simple example in this paper to show how to use V.PhyloMaker to generate phylogenies.", url = "https://doi.org/10.1111/ecog.04434", doi = "10.1111/ecog.04434", openalex = "W2922439782", references = "doi101038nature12872" } @article{doi101111gcb14904, author = "Kattge, Jens and Bönisch, Gerhard and Dı́az, Sandra and Lavorel, Sandra and Prentice, I. Colin and Leadley, Paul and Tautenhahn, Susanne and Werner, Gijsbert D. A. and Aakala, Tuomas and Abedi, Mehdi and Acosta, Alicia Teresa Rosario and Adamidis, George C. and Adamson, Kairi and Aiba, Masahiro and Albert, Cécile H. and Alcántara, Julio M. and C, Carolina Alcázar and Aleixo, Izabela and Ali, Hamada E. and Amiaud, Bernard and Ammer, Christian and Amoroso, Mariano M. and Anand, Madhur and Anderson, C. and Anten, Niels P. R. and Antos, Joseph A. and Apgaua, Deborah M. G. and Ashman, Tia‐Lynn and Asmara, Degi Harja and Asner, Gregory P. and Aspinwall, Michael J. and Atkin, Owen K. and Aubin, Isabelle and Baastrup‐Spohr, Lars and Bahalkeh, Khadijeh and Bahn, Michael and Baker, Timothy R. and Baker, William J. and Bakker, Jan P. and Baldocchi, Dennis and Baltzer, Jennifer L. and Banerjee, Arindam and Baranger, Anne and Barlow, Jos and Barneche, Diego R. and Baruch, Zdravko and Bastianelli, Denis and Battles, John J. and Bauerle, William L. and Bauters, Marijn and Bazzato, Erika and Beckmann, Michael and Beeckman, Hans and Beierkuhnlein, Carl and Bekker, Renée M. and Belfry, Gavin and Belluau, Michaël and Beloiu, Mirela and Benavides, Raquel and Benomar, Lahcen and Berdugo‐Lattke, Mary Lee and Berenguer, Erika and Bergamin, Rodrigo Scarton and Bergmann, Joana and Carlucci, Marcos Bergmann and Berner, Logan T. and Bernhardt‐Römermann, Markus and Bigler, Christof and Bjorkman, Anne D. and Blackman, Chris J. and Blanco, C. and Blonder, Benjamin and Blumenthal, Dana M. and Bocanegra‐González, Kelly T. and Boeckx, Pascal and Bohlman, Stephanie and Böhning‐Gaese, Katrin and Boisvert‐Marsh, Laura and Bond, William J. and Bond‐Lamberty, Ben and Boom, Arnoud and Boonman, Coline C. F. and Bordin, Kauane Maiara and Boughton, Elizabeth H. and Boukili, Vanessa and Bowman, David M. J. S. and Bravo, Sandra and Brendel, Marco R. and Broadley, Martin R. and Brown, Kerry A. and Bruelheide, Helge and Brumnich, Federico and Bruun, Hans Henrik and Bruy, David and Buchanan, Serra-Willow and Bucher, Solveig Franziska and Buchmann, Nina and Buitenwerf, Robert and Bunker, Daniel E. and Bürger, Jana", title = "TRY plant trait database – enhanced coverage and open access", year = "2019", journal = "Global Change Biology", abstract = "Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.", url = "https://doi.org/10.1111/gcb.14904", doi = "10.1111/gcb.14904", openalex = "W2983606184", references = "doi101038nature12872, doi101038ncomms5087, doi101038s4158601805637, doi101071bt12225, doi101111j13652486201102451x, doi101111j14610248200801219x, doi101111j14610248200901285x" } @article{doi101111ele13584, author = "Sanchez‐Martinez, Pablo and Martínez‐Vilalta, Jordi and Dexter, Kyle G. and Segovia, Ricardo A. and Mencuccini, Maurizio", title = "Adaptation and coordinated evolution of plant hydraulic traits", year = "2020", journal = "Ecology Letters", abstract = "Hydraulic properties control plant responses to climate and are likely to be under strong selective pressure, but their macro-evolutionary history remains poorly characterised. To fill this gap, we compiled a global dataset of hydraulic traits describing xylem conductivity (K s), xylem resistance to embolism (P50), sapwood allocation relative to leaf area (Hv) and drought exposure (ψ min), and matched it with global seed plant phylogenies. Individually, these traits present medium to high levels of phylogenetic signal, partly related to environmental selective pressures shaping lineage evolution. Most of these traits evolved independently of each other, being co-selected by the same environmental pressures. However, the evolutionary correlations between P50 and ψ min and between K s and Hv show signs of deeper evolutionary integration because of functional, developmental or genetic constraints, conforming to evolutionary modules. We do not detect evolutionary integration between conductivity and resistance to embolism, rejecting a hardwired trade-off for this pair of traits.", url = "https://doi.org/10.1111/ele.13584", doi = "10.1111/ele.13584", openalex = "W3073875730", references = "doi101098rspb20181012" } @incollection{crossref2021angiosperms, title = "ANGIOSPERMS:", year = "2021", booktitle = "The Ecology of the Trees, Shrubs, and Woody Vines of Northern Florida", url = "https://doi.org/10.2307/j.ctv1t1kg94.10", doi = "10.2307/j.ctv1t1kg94.10", pages = "57-360" } @article{doi101111nph17822, author = "Benton, Michael J. and Wilf, Peter and Sauquet, Hervé", title = "The Angiosperm Terrestrial Revolution and the origins of modern biodiversity", year = "2021", journal = "New Phytologist", abstract = "Biodiversity today has the unusual property that 85\% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial diversity occurred from c. 100-50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction; coevolution with animals, especially pollinators and herbivores; photosynthetic capacities; adaptability; and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.", url = "https://doi.org/10.1111/nph.17822", doi = "10.1111/nph.17822", openalex = "W3209026994", references = "doi101016jcub201508003, doi101016jcub201804062, doi101016jgloplacha201804004, doi101016jtree201905008, doi101038nature06277, doi101038ncomms16047, doi101038s4158601916932, doi101073pnas1112694108, doi101073pnas1813206116, doi101073pnas1907847116, doi101093icbicq078, doi101093molbevmsx324, doi101093sysbiosyaa034, doi101098rspb20080715, doi101111syen12132, doi1023072399030, doi103390ijms140510242, doi1034172009143, doi107717peerj1719" } @article{doi101016jpld202205005, author = "Jin, Yi and Qian, Hong", title = "V.PhyloMaker2: An updated and enlarged R package that can generate very large phylogenies for vascular plants", year = "2022", journal = "Plant Diversity", abstract = "An earlier version of V.PhyloMaker has been broadly used to generate phylogenetic trees of vascular plants for botanical, biogeographical and ecological studies. Here, we update and enlarge this package, which is now called 'V.PhyloMaker2'. With V.PhyloMaker2, one can generate a phylogenetic tree for vascular plants based on one of three different botanical nomenclature systems. V.PhyloMaker2 can generate phylogenies for very large species lists (the largest species list that we tested included 365,198 species). V.PhyloMaker2 generates phylogenies at a fast speed. We provide an example (including a sample species list and an R script to run it) in this paper to show how to use V.PhyloMaker2 to generate phylogenetic trees.", url = "https://doi.org/10.1016/j.pld.2022.05.005", doi = "10.1016/j.pld.2022.05.005", openalex = "W4281979425", references = "doi101038nature12872" } @article{doi101038s41477022011297, author = "Liu, Yang and Wang, Sibo and Li, Linzhou and Yang, Ting and Dong, Shanshan and Wei, Tong and Wu, Shengdan and Liu, Yongbo and Gong, Yiqing and Feng, Xiuyan and Ma, Jianchao and Chang, Guanxiao and Huang, Jinling and Yang, Yong and Wang, Hongli and Liu, Min and Xu, Yan and Liang, Hongping and Jin, Yu and Cai, Yuqing and Zhang, Zhaowu and Fan, Yannan and Mu, Weixue and Sahu, Sunil Kumar and Liu, Shuchun and Lang, Xiaoan and Yang, Leilei and Li, Na and Habib, Sadaf and Yang, Yongqiong and Lindström, Anders J. and Liang, Pei and Goffinet, Bernard and Zaman, Sumaira and Wegrzyn, Jill and Li, Dexiang and Liu, Jian and Cui, Jie and Sonnenschein, Eva C. and Wang, Xiaobo and Ruan, Jue and Xue, Jia‐Yu and Shao, Zhu‐Qing and Song, Chi and Fan, Guangyi and Li, Zhen and Zhang, Liangsheng and Liu, Jianquan and Liu, Zhong‐Jian and Jiao, Yuannian and Wang, Xiaoquan and Wu, Hong and Wang, Ertao and Lisby, Michael and Yang, Huanming and Wang, Jian and Liu, Xin and Xu, Xun and Li, Nan and Soltis, Pamela S. and de Peer, Yves Van and Soltis, Douglas E. and Gong, Xun and Liu, Huan and Zhang, Shouzhou", title = "The Cycas genome and the early evolution of seed plants", year = "2022", journal = "Nature Plants", abstract = "Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.", url = "https://doi.org/10.1038/s41477-022-01129-7", doi = "10.1038/s41477-022-01129-7", openalex = "W4223990635", references = "doi101098rspb20181012" } @misc{crossrefNoneangiosperms, title = "Angiosperms", year = "None", booktitle = "AccessScience", url = "https://doi.org/10.1036/1097-8542.yb010070", doi = "10.1036/1097-8542.yb010070" }