Abstract：
PREMISE OF THE STUDY:Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants. METHODS:We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta. We constructed phylogenies of major clades, estimated divergence times, and incorporated data from the Open Tree of Life project, resulting in a seed plant phylogeny. We estimated diversification rates, excluding those taxa without molecular data. We also summarized topological uncertainty and data overlap for each major clade. KEY RESULTS:The trees constructed for Spermatophyta consisted of 79,881 and 353,185 terminal taxa; the latter included the Open Tree of Life taxa for which we could not include molecular data from GenBank. The diversification analyses demonstrated nested patterns of rate shifts throughout the phylogeny. Data overlap and inference uncertainty show significant variation throughout and demonstrate the continued need for data collection across seed plants. CONCLUSIONS: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.
journal_name
Am J Botjournal_title
American journal of botanyauthors
Smith SA,Brown JWdoi
10.1002/ajb2.1019subject
Has Abstractpub_date
2018-03-01 00:00:00pages
302-314issue
3eissn
0002-9122issn
1537-2197journal_volume
105pub_type
杂志文章abstract：:Isozymatic data taken from 67 Guatemalan collections of maize were subjected to numerical taxonomic analyses to elucidate systematic relationships among the 19 maize races and subraces described for Guatemala by Wellhausen et al. As with Bolivian and Mexican races, isozymatic variation in Guatemalan maize was strongly...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.1002/j.1537-2197.1990.tb13547.x
更新日期：1990-02-01 00:00:00
abstract：:Koch et al. (Nature 428: 851-854) measured various parameters that were thought to limit the height of Sequoia sempervirens from northern California and concluded that the maximum height for this species is 122-130 m because within this range: (1) Irreversible embolism formation was proposed to occur when the xylem pr...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.0800144
更新日期：2009-02-01 00:00:00
abstract：:A detailed study of ascomal morphology and development in Cercophora palmicola showed that ontogeny is ascohymeniaceous, giving rise to an ostiolate perithecium. Ascomal initials consist of a coiled ascogonium surrounded by several layers of hyphae whose cells become pseudoparenchymatous. The centrum of the young asco...
journal_title：American journal of botany
pub_type： 杂志文章
doi：
更新日期：1999-06-01 00:00:00
abstract：:The American chestnut (Castanea dentata; Fagaceae) was a dominant canopy tree in the Appalachian Mountains of North America. Since the introduction of the chestnut blight fungus (Cryphonectria parasitica; Valsaceae) in America, the American chestnut has been reduced to a predominantly clonal, understory species. Our o...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.90.2.207
更新日期：2003-02-01 00:00:00
abstract：UNLABELLED: PREMISE OF STUDY:Phylogenetic relationships of the papilionoid legumes (Papilionoideae) reveal that the early branches are more highly diverse in floral morphology than are other clades of Papilionoideae. This study attempts for the first time to comprehensively sample the early-branching clades of this ec...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1200380
更新日期：2012-12-01 00:00:00
abstract：:Very little is known regarding how repetitive elements evolve inpolyploid organisms. Here we address this subject by fluorescent insitu hybridization (FISH) of 20 interspersed repetitive elements tometaphase chromosomes of the cotton AD-genome tetraploid Gossypiumhirsutum and its putative A- and D-genome diploid ances...
journal_title：American journal of botany
pub_type： 杂志文章
doi：
更新日期：1998-10-01 00:00:00
abstract：PREMISE OF THE STUDY:Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and bi...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1600177
更新日期：2016-09-01 00:00:00
abstract：:We used the chloroplast gene ndhF to reconstruct the phylogeny of the moonseed family (Menispermaceae), a morphologically diverse and poorly known cosmopolitan family of dioecious, primarily climbing plants. This study includes a worldwide sample of DNA sequences for 88 species representing 49 of the 70 genera of all ...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.94.8.1425
更新日期：2007-08-01 00:00:00
abstract：PREMISE OF THE STUDY:Climate change models for California predict a warmer, drier future, potentially resulting in shorter growing seasons. If phenotypic differences between closely related species currently distributed across a moisture and temperature gradient represent adaptations to their abiotic environment, then ...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1500108
更新日期：2016-01-01 00:00:00
abstract：:Aralia sect. Aralia (Araliaceae) consists of approximately eight species disjunctly distributed in Asia and North America. Phylogenetic and biogeographic analyses were conducted using sequences of the internal transcribed spacer regions of the nuclear ribosomal DNA. Aralia racemosa from eastern North America was siste...
journal_title：American journal of botany
pub_type： 杂志文章
doi：
更新日期：1998-06-01 00:00:00
abstract：:Interspecific hybridization is considered a possible mechanism of plant diversification. The Andes are a hotspot of biodiversity, but hybridization in Andean taxa has so far not been investigated intensively. The current study investigates crossability in Caiophora (Loasaceae subfam. Loasoideae) by experimental inters...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.2007403
更新日期：2008-09-01 00:00:00
abstract：PREMISE OF THE STUDY:Direct tests of a species distribution model (SDM) were used to evaluate the hypothesis that the northern and southern edges of Mimulus bicolor's geographical range are limited by temperature and precipitation. METHODS:Climatic suitability was predicted using an SDM informed only by temperature an...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1600414
更新日期：2017-06-01 00:00:00
abstract：:We assessed the effects of local environment on survival, growth, and development in six clones (genotypes) of Vallisneria americana grown at five sites in the Huron-Erie Corridor. Detrimental effects of local environment on plant performance (rate of clonal growth, leaf and root production, surface area of leaves and...
journal_title：American journal of botany
pub_type： 杂志文章
doi：
更新日期：1997-12-01 00:00:00
abstract：:The temperature dependence of freezing-induced xylem cavitation was studied in a Chihuahuan desert population of Larrea tridentata (Zygophyllaceae). Field measurements of wood temperature and xylem embolism were combined with anatomical studies and laboratory measurements of embolism in stem and root samples frozen un...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.89.12.1916
更新日期：2002-12-01 00:00:00
abstract：:Self-incompatibility (SI) is an effective method for limiting self-fertilization in flowering plant species, but there are circumstances in which an otherwise functional SI system may fail. One of the most intriguing of these is the induction of selfing by mixed loads of self and heterospecific pollen (the mentor effe...
journal_title：American journal of botany
pub_type： 杂志文章
doi：
更新日期：1998-06-01 00:00:00
abstract：:The specific shape of the relationship between plant diversity and productivity and the causal mechanism(s) behind the observed pattern(s) are still highly debated. Recent advances suggest that the relationship depends on several environmental variables and may change with the observational scale. In this study, a mul...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.94.1.79
更新日期：2007-01-01 00:00:00
abstract：:Soybean partial-female-sterile mutant 1 (PS-1) was recovered from a gene-tagging study. The objectives were to study the inheritance, linkage, allelism, and certain aspects of the reproductive biology of the PS-1 mutant. For inheritance and linkage tests, PS-1 was crossed to flower color mutant Harosoy-w4 and to chlor...
journal_title：American journal of botany
pub_type： 杂志文章
doi：
更新日期：1997-06-01 00:00:00
abstract：:There have been three periods of significant discovery in the exploration of fern and lycophyte genetics. First, during the 1930s, Andersson-Kottö conducted crossing studies on ferns. The publication of Manton's magnum opus on fern chromosomes in 1950 stimulated the second. The third emerged from Klekowski's 1973 Amer...
journal_title：American journal of botany
pub_type： 杂志文章,评审
doi：10.3732/ajb.1400317
更新日期：2014-12-01 00:00:00
abstract：PREMISE OF THE STUDY:Plant communities may be influenced by toxic secondary metabolites or enhanced plant growth from plant-symbiont interactions. The C:N hypothesis predicts that carbon or nitrogen constrains plant secondary metabolite production, but it does not consider compounds produced by plant symbionts. Locowee...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1100133
更新日期：2011-12-01 00:00:00
abstract：PREMISE OF THE STUDY:New microsatellite primers were developed for testing genetic differentiation within Nothoceros aenigmaticus and their potential use in other Nothoceros species. The microsatellites are designed to investigate partitioning of genetic variation in a taxon with a peculiar sex allopatry in the souther...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1100392
更新日期：2012-03-01 00:00:00
abstract：PREMISE OF THE STUDY:Gravity has been a major force throughout the evolution of terrestrial organisms, and plants have developed exquisitely sensitive, regulated tropisms and growth patterns that are based on the gravity vector. The nullified gravity during spaceflight allows direct assessment of gravity roles. The mic...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1200343
更新日期：2013-01-01 00:00:00
abstract：PREMISE OF THE STUDY:Inclusion of fossils in phylogenetic analyses is necessary in order to construct a comprehensive "tree of death" and elucidate evolutionary history of taxa; however, such incorporation of fossils in phylogenetic reconstruction is dependent on the availability and interpretation of extensive morphol...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.1002/ajb2.1123
更新日期：2018-08-01 00:00:00
abstract：UNLABELLED:• PREMISE OF THE STUDY:The ability to respond to environmental change via phenotypic plasticity may be important for plants experiencing disturbances such as climate change and plant invasion. Responding to belowground competition through root plasticity may allow native plants to persist in highly invaded ...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1400234
更新日期：2015-01-01 00:00:00
abstract：PREMISE OF THE STUDY:Virtually nothing is known about what actually happens during prolonged dormancy, the period during which significant proportions of geophyte populations do not sprout after seasonal dormancy but remain alive underground, to emerge again 1 or more years later. This study investigated the fate of pe...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1000262
更新日期：2011-02-01 00:00:00
abstract：:Primarily known only by the edible fruits of Citrus, Rutaceae comprise a large (c. 160 genera and 1900 species), morphologically diverse, cosmopolitan family. Of its extraordinary array of secondary chemical compounds, many have medicinal, antimicrobial, insecticidal, or herbicidal properties. To assist with the much-...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.2007313
更新日期：2008-08-01 00:00:00
abstract：PREMISE:Declines in reproductive capabilities with increasing age are common across the tree of life. However, in plants, mating system traits have rarely been tested for signs of senescence. Since reproduction is often resource limited, we might expect outcrossing and selfing taxa to allocate these resources different...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.1002/ajb2.1346
更新日期：2019-09-01 00:00:00
abstract：UNLABELLED: PREMISE OF THE STUDY:Diversification of floral traits in angiosperms is often attributed to have been driven by adaptations to pollinators. Nevertheless, phylogenetic studies on the relationships among evolutionary changes in floral traits and pollination systems are still limited. We examined the relation...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1200359
更新日期：2013-03-01 00:00:00
abstract：PREMISE OF THE STUDY:Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) a...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1500079
更新日期：2016-01-01 00:00:00
abstract：PREMISE OF THE STUDY:We isolated and characterized microsatellite markers for the California poppy, Eschscholzia californica, which is an invasive species in central Chile. METHODS AND RESULTS:A total of eight polymorphic and six monomorphic loci were developed for the species. Between one and 12 alleles were observed...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.1200076
更新日期：2012-09-01 00:00:00
abstract：:Propagule banks are assumed to be able to store considerable genetic variability. Bryophyte populations are expected to rely more heavily on stored propagules than those of seed plants due to the vulnerability of the haploid gametophyte. This reliance has important implications for the genetic structure and evolutiona...
journal_title：American journal of botany
pub_type： 杂志文章
doi：10.3732/ajb.2007283
更新日期：2008-05-01 00:00:00
