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1.
Am J Bot ; 2020 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-32596837

RESUMO

PREMISE: Undoubtedly, fossils are critical for understanding evolutionary transformations in deep time. Here, we reinvestigate the microspores and megaspores of Paleoazolla patagonica, a water fern found in Late Cretaceous sediments of the Chubut Province, Patagonia, Argentina, which provides novel evidence on the past history of the water fern clade. The study was based on recently collected specimens and additional observations of the original material. METHODS: Most specimens analyzed herein were obtained from new palynological samples collected at the Cerro Bosta and Cañadón del Irupé localities, La Colonia Formation. Samples were mechanically disaggregated and treated with hydrofluoric and hydrochloric acid. Spores were studied using standard light microscopy and scanning electron microscopy. We also reexamined the original materials. RESULTS: The newly described characters of Paleoazolla include the presence of heterosporangiate sori composed of one ellipsoidal megasporangium surrounded by three to four oval microsporangia, megasporangium containing one hairy massula that encloses two trilete megaspores (rarely one or three), and microsporangia containing numerous microspore massulae with non-septate multibarbed glochidia and one trilete microspore per massula. CONCLUSIONS: The reinterpretation has revealed a novel set of characters for understanding the evolution of heterosporous water ferns. The presence of two megaspores in the megasporangium of Paleoazolla exposes serious gaps in the current knowledge on the evolution of monomegaspory in heterosporous water ferns, a fact that emphasizes the need of including fossils within phylogenies to elucidate patterns of character acquisition among water ferns.

2.
Science ; 366(6467)2019 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-31727802

RESUMO

Denk et al agree that we reported the first fossil Fagaceae from the Southern Hemisphere. We appreciate their general enthusiasm for our findings, but we reject their critiques, which we find misleading and biased. The new fossils unequivocally belong to Castanopsis, and substantial evidence supports our Southern Route to Asia hypothesis.


Assuntos
Fagaceae , Floresta Úmida , Ásia , Fósseis
3.
Science ; 364(6444)2019 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-31171664

RESUMO

The beech-oak family Fagaceae dominates forests from the northern temperate zone to tropical Asia and Malesia, where it reaches its southern limit. We report early Eocene infructescences of Castanopsis, a diverse and abundant fagaceous genus of Southeast Asia, and co-occurring leaves from the 52-million-year-old Laguna del Hunco flora of southern Argentina. The fossil assemblage notably includes many plant taxa that associate with Castanopsis today. The discovery reveals novel Gondwanan history in Fagaceae and the characteristic tree communities of Southeast Asian lower-montane rainforests. The living diaspora associations persisted through Cenozoic climate change and plate movements as the constituent lineages tracked post-Gondwanan mesic biomes over thousands of kilometers, underscoring their current vulnerability to rapid climate change and habitat loss.


Assuntos
Evolução Biológica , Fagaceae/classificação , Fósseis , Floresta Úmida , Argentina , Ásia , Chile , Mudança Climática , Folhas de Planta
4.
Am J Bot ; 105(11): 1888-1910, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30368769

RESUMO

PREMISE OF THE STUDY: We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS: We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS: Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS: We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).


Assuntos
Especiação Genética , Genomas de Plastídeos , Magnoliopsida/genética , Filogenia , DNA Intergênico , Zingiberales/genética
5.
Am J Bot ; 105(6): 1067-1087, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29995329

RESUMO

PREMISE OF THE STUDY: We describe a new araucarian species, Araucaria lefipanensis, from the Late Cretaceous flora of the Lefipán Formation, in Patagonia (Argentina) based on reproductive and vegetative remains, with a combination of characters that suggest mosaic evolution in the Araucaria lineage. METHODS: The studied fossils were found at the Cañadón del Loro locality. Specimens were separated into two leaf morphotypes, and their morphological differences were tested with MANOVA. KEY RESULTS: The new species Araucaria lefipanensis is erected based on the association of dimorphic leaves with cuticle remains and isolated cone scale complexes. The reproductive morphology is characteristic of the extant section Eutacta, whereas the vegetative organs resemble those of the sections Intermedia, Bunya, and Araucaria (the broad-leaved clade). CONCLUSIONS: The leaf dimorphism of A. lefipanensis is similar to that of extant A. bidwillii, where dimorphism is considered to be related to seasonal growth. The leaf dimorphism in A. lefipanensis is consistent with the paleoclimatic and paleoenvironmental reconstructions previously suggested for the Lefipán Formation, which is thought to have been a seasonal subtropical forest. The new species shows evidence of mosaic evolution, with cone scale complexes morphologically similar to section Eutacta and leaves similar to the sections of the broad-leaved clade, constituting a possible transitional form between these two well-defined lineages. More complete plant concepts, especially those including both reproductive and vegetative remains are necessary to understand the evolution of ancient plant lineages. This work contributes to this aim by documenting a new species that may add to the understanding of the early evolution of the sections of Araucaria.


Assuntos
Fósseis , Traqueófitas/anatomia & histologia , Argentina , Folhas de Planta/anatomia & histologia
6.
Am J Bot ; 105(8): 1424-1435, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29901855

RESUMO

PREMISE OF THE STUDY: An inflorescence with three pistillate flowers in amber from the early Upper Cretaceous (Turonian, ~90-94 million years ago) of central New Jersey represents the oldest known flowers with features present in an early stem complex of the Fagales. The inflorescence has characteristics of Nothofagaceae, but also has strikingly distinct characters that suggest it is intermediate between Nothofagus and other Fagales. This intermediacy is consistent with its northern hemisphere distribution. METHODS: We investigated this new fossil by comparing it with extant and fossil members of the Fagales using light microscopy and nano-computed tomography. In addition, for exploring its relationships, we mapped the morphological characters onto a widely accepted molecular-based tree of modern basal Fagales using standard methods of character optimization. KEY RESULTS: The phylogenetic position of the fossil inflorescence can be unequivocally determined by the presence of unique features, singly and in combination, that are found only in "basal" members of Fagales. The fossil adds critical information on the features of the early stem Fagales, evolution of the cupule in Nothofagaceae and Fagaceae, and a reasonable biogeographic hypothesis for the differentiation of southern (e.g., Nothofagaceae) and northern hemisphere Fagales. CONCLUSIONS: This new fossil provides insight into the early evolution of Fagales and suggests that early stem Fagales that had not yet differentiated into modern families were present in the Late Cretaceous of North America. Based on available evidence, the fossil is best interpreted as an early stem member of the Fagales, with features that suggest a transition from a more generalized Nothofagus-like fagalean ancestor with some unique presumably plesiomorphic features. The presence of an enlarged perianth and flexuous styles also suggests the possibility of insect pollination, which has been lost in all Fagales with the exception of some members of subfamily Castaneoideae in Fagaceae sensu stricto (which otherwise are very different from this fossil). The poorly developed, bract-like cupule valves of the fossil can be interpreted as primitive (i.e., incipient) or as reduced from more developed cupules that are found in most modern Fagaceae and Nothofagaceae.


Assuntos
Fagales/anatomia & histologia , Fósseis , Inflorescência/anatomia & histologia , Âmbar , New Jersey
7.
Am J Bot ; 105(5): 927-942, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29882954

RESUMO

PREMISE OF THE STUDY: The fossil record is critical for testing biogeographic hypotheses. Menispermaceae (moonseeds) are a widespread family with a rich fossil record and alternative hypotheses related to their origin and diversification. The family is well-represented in Cenozoic deposits of the northern hemisphere, but the record in the southern hemisphere is sparse. Filling in the southern record of moonseeds will improve our ability to evaluate alternative biogeographic hypotheses. METHODS: Fossils were collected from the Salamanca (early Paleocene, Danian) and the Huitrera (early Eocene, Ypresian) formations in Chubut Province, Argentina. We photographed them using light microscopy, epifluorescence, and scanning electron microscopy and compared the fossils with similar extant and fossil Menispermaceae using herbarium specimens and published literature. KEY RESULTS: We describe fossil leaves and endocarps attributed to Menispermaceae from Argentinean Patagonia. The leaves are identified to the family, and the endocarps are further identified to the tribe Cissampelideae. The Salamancan endocarp is assigned to the extant genus Stephania. These fossils significantly expand the known range of Menispermaceae in South America, and they include the oldest (ca. 64 Ma) unequivocal evidence of the family worldwide. CONCLUSIONS: Our findings highlight the importance of West Gondwana in the evolution of Menispermaceae during the Paleogene. Currently, the fossil record does not discern between a Laurasian or Gondwanan origin; however, it does demonstrate that Menispermaceae grew well outside the tropics by the early Paleocene. The endocarps' affinity with Cissampelideae suggests that diversification of the family was well underway by the earliest Paleocene.


Assuntos
Fósseis/anatomia & histologia , Menispermaceae/anatomia & histologia , Menispermaceae/classificação , Argentina , Fósseis/ultraestrutura , Frutas/anatomia & histologia , Frutas/classificação , Frutas/ultraestrutura , Menispermaceae/ultraestrutura , Microscopia Eletrônica de Varredura , Dispersão Vegetal , Folhas de Planta/anatomia & histologia , Folhas de Planta/classificação , Folhas de Planta/ultraestrutura
8.
Ann Bot ; 121(3): 431-442, 2018 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-29309506

RESUMO

Background and Aims: Early Palaeocene (Danian) plant fossils from Patagonia provide information on the recovery from the end-Cretaceous extinction and Cenozoic floristic change in South America. Actinomorphic flowers with eight to ten perianth parts are described and evaluated in a phylogenetic framework. The goal of this study is to determine the identity of these fossil flowers and to discuss their evolutionary, palaeoecological and biogeographical significance. Methods: More than 100 fossilized flowers were collected from three localities in the Danian Salamanca and Peñas Coloradas Formations in southern Chubut. They were prepared, photographed and compared with similar extant and fossil flowers using published literature and herbarium specimens. Phylogenetic analysis was performed using morphological and molecular data. Key results: The fossil flowers share some but not all the synapomorphies that characterize the Schizomerieae, a tribe within Cunoniaceae. These features include the shallow floral cup, variable number of perianth parts arranged in two whorls, laciniate petals, anthers with a connective extension, and a superior ovary with free styles. The number of perianth parts is doubled and the in situ pollen is tricolporate, with a surface more like that of other Cunoniaceae outside Schizomerieae, such as Davidsonia or Weinmannia. Conclusions: An extinct genus of crown-group Cunoniaceae is recognized and placed along the stem lineage leading to Schizomerieae. Extant relatives are typical of tropical to southern-temperate rainforests, and these fossils likely indicate a similarly warm and wet temperate palaeoclimate. The oldest reliable occurrences of the family are fossil pollen and wood from the Upper Cretaceous of the Antarctica and Argentina, whereas in Australia the family first occurs in upper Palaeocene deposits. This discovery demonstrates that the family survived the Cretaceous-Palaeogene boundary event in Patagonia and that diversification of extant lineages in the family was under way by the earliest Cenozoic.


Assuntos
Flores/anatomia & histologia , Fósseis/anatomia & histologia , Magnoliopsida/anatomia & histologia , Argentina , História Antiga , Filogenia
9.
PLoS One ; 12(5): e0176164, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28489895

RESUMO

Southern-Hemisphere terrestrial communities from the early Paleocene are poorly known, but recent work on Danian plant fossils from the Salamanca Formation in Chubut Province, Argentina are providing critical data on earliest Paleocene floras. The fossils described here come from a site in the Salamanca Formation dating to ca. 1 million years or less after the end-Cretaceous extinction event; they are the first fossil flowers reported from the Danian of South America, and possible the entire Southern Hemisphere. They are compressions and impressions in flat-laminated light gray shale, and they belong to the family Rhamnaceae (buckthorns). Flowers of Notiantha grandensis gen. et sp. nov. are pentamerous, with distinctly keeled calyx lobes projecting from the hypanthium, clawed and cucullate emarginate petals, antepetalous stamens, and a pentagonal floral disk that fills the hypanthium. Their phylogenetic position was evaluated using a molecular scaffold approach combined with morphological data. Results indicate that the flowers are most like those of extant ziziphoid Rhamnaceae. The associated leaves, assigned to Suessenia grandensis gen. et sp. nov. are simple and ovate, with serrate margins and three acrodromous basal veins. They conform to the distinctive leaves of some extant Rhamnaceae in the ziziphoid and ampelozizyphoid clades. These fossils provide the first unequivocal megafossil evidence of Rhamnaceae in the Southern Hemisphere, demonstrating that Rhamnaceae expanded beyond the tropics by the earliest Paleocene. Given previous reports of rhamnaceous pollen in the late Paleogene and Neogene of Antarctica and southern Australia, this new occurrence increases the possibility of high-latitude dispersal of this family between South America and Australia via Antarctica during the Cenozoic.


Assuntos
Flores/crescimento & desenvolvimento , Folhas de Planta/crescimento & desenvolvimento , Argentina , Fósseis , Geologia
10.
Ann Bot ; 119(4): 507-516, 2017 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-28110267

RESUMO

Background and Aims: Radially symmetrical, five-winged fossil fruits from the highly diverse early Eocene Laguna del Hunco flora of Chubut Province, Patagonia, Argentina, are named, described and illustrated. The main goals are to assess the affinities of the fossils and to place them in an evolutionary, palaeoecological and biogeographic context. Methods: Specimens of fossil fruits were collected from the Tufolitas Laguna del Hunco. They were prepared, photographed and compared with similar extant and fossil fruits using published literature. Their structure was also evaluated by comparing them with that of modern Ceratopetalum (Cunoniaceae) fruits through examination of herbarium specimens. Key Results: The Laguna del Hunco fossil fruits share the diagnostic features that characterize modern and fossil Ceratopetalum (symmetry, number of fruit wings, presence of a conspicuous floral nectary and overall venation pattern). The pattern of the minor wing (sepal) veins observed in the Patagonian fossil fruits is different from that of modern and previously described fossil Ceratopetalum fruits; therefore, a new fossil species is recognized. An apomorphy (absence of petals) suggests that the fossils belong within crown-group Ceratopetalum . Conclusions: The Patagonian fossil fruits are the oldest known record for Ceratopetalum . Because the affinities, provenance and age of the fossils are so well established, this new Ceratopetalum fossil species is an excellent candidate for use as a calibration point in divergence dating studies of the family Cunoniaceae. It represents the only record of Ceratopetalum outside Australasia, and further corroborates the biogeographic connection between the Laguna del Hunco flora and ancient and modern floras of the Australasian region.


Assuntos
Fósseis/anatomia & histologia , Frutas/anatomia & histologia , Oxalidaceae/anatomia & histologia , Argentina , Evolução Biológica , Flores/anatomia & histologia
11.
Science ; 355(6320): 71-75, 2017 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-28059765

RESUMO

The nightshade family Solanaceae holds exceptional economic and cultural importance. The early diversification of Solanaceae is thought to have occurred in South America during its separation from Gondwana, but the family's sparse fossil record provides few insights. We report 52.2-million-year-old lantern fruits from terminal-Gondwanan Patagonia, featuring highly inflated, five-lobed calyces, as a newly identified species of the derived, diverse New World genus Physalis (e.g., groundcherries and tomatillos). The fossils are considerably older than corresponding molecular divergence dates and demonstrate an ancient history for the inflated calyx syndrome. The derived position of these early Eocene fossils shows that Solanaceae were well diversified long before final Gondwanan breakup.


Assuntos
Frutas/classificação , Physalis/classificação , Argentina , Chile , Fósseis , Frutas/anatomia & histologia , Filogenia , Filogeografia , Physalis/anatomia & histologia
12.
Am J Bot ; 104(9): 1344-1369, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-29885237

RESUMO

PREMISE OF THE STUDY: The flip-leaved podocarp Retrophyllum has a disjunct extant distribution in South American and Australasian tropical rainforests and a Gondwanic fossil record since the Eocene. Evolutionary, biogeographic, and paleoecological insights from previously described fossils are limited because they preserve little foliar variation and no reproductive structures. METHODS: We investigated new Retrophyllum material from the terminal Cretaceous Lefipán, the early Eocene Laguna del Hunco, and the early/middle Eocene Río Pichileufú floras of Patagonian Argentina. We also reviewed type material of historical Eocene fossils from southern Chile. KEY RESULTS: Cretaceous Retrophyllum superstes sp. nov. is described from a leafy twig, while Eocene R. spiralifolium sp. nov. includes several foliage forms and a peduncle with 13 pollen cones. Both species preserve extensive damage from sap-feeding insects associated with foliar transfusion tissue. The Eocene species exhibits a suite of characters linking it to both Neotropical and West Pacific Retrophyllum, along with several novel features. Retrophyllum araucoensis (Berry) comb. nov. stabilizes the nomenclature for the Chilean fossils. CONCLUSIONS: Retrophyllum is considerably older than previously thought and is a survivor of the end-Cretaceous extinction. Much of the characteristic foliar variation and pollen-cone morphology of the genus evolved by the early Eocene. The mixed biogeographic signal of R. spiralifolium supports vicariance and represents a rare Neotropical connection for terminal-Gondwanan Patagonia, which is predominantly linked to extant Australasian floras due to South American extinctions. The leaf morphology of the fossils suggests significant drought vulnerability as in living Retrophyllum, indicating humid paleoenvironments.


Assuntos
Fósseis/anatomia & histologia , Folhas de Planta/anatomia & histologia , Traqueófitas/anatomia & histologia , Argentina , Herbivoria
13.
PLoS One ; 9(8): e104749, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25148081

RESUMO

In this contribution, we describe latest Cretaceous aquatic plant communities from the La Colonia Formation, Patagonia, Argentina, based on their taxonomic components and paleoecological attributes. The La Colonia Formation is a geological unit deposited during a Maastrichtian-Danian transgressive episode of the South Atlantic Ocean. This event resulted in the deposition of a series of fine-grained sediments associated with lagoon systems occurring along irregular coastal plains in northern Patagonia. These deposits preserved a diverse biota, including aquatic and terrestrial plants and animals. The aquatic macrophytes can be broadly divided into two groups: free-floating and rooted, the latter with emergent or floating leaves. Free-floating macrophytes include ferns in Salviniaceae (Azolla and Paleoazolla) and a monocot (Araceae). Floating microphytes include green algae (Botryoccocus, Pediastrum and Zygnemataceae). Among the rooted components, marsileaceous water ferns (including Regnellidium and an extinct form) and the eudicot angiosperm Nelumbo (Nelumbonaceae) are the dominant groups. Terrestrial plants occurring in the vegetation surrounding the lagoons include monocots (palms and Typhaceae), ferns with affinities to Dicksoniaceae, conifers, and dicots. A reconstruction of the aquatic plant paleocommuniy is provided based on the distribution of the fossils along a freshwater horizon within the La Colonia Formation. This contribution constitutes the first reconstruction of a Cretaceous aquatic habitat for southern South America.


Assuntos
Organismos Aquáticos , Ecossistema , Plantas , Organismos Aquáticos/classificação , Argentina , Geografia , Magnoliopsida/classificação , Magnoliopsida/ultraestrutura , Plantas/classificação , Dinâmica Populacional
14.
Am J Bot ; 100(9): 1831-48, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24018858

RESUMO

PREMISE OF THE STUDY: The early Eocene Laguna del Hunco caldera-lake paleoflora (ca. 52 Ma) from Chubut Province, Argentina, is notably diverse and includes many conifer and angiosperm lineages that are extinct in South America but extant in Australasian rainforests. No ferns have been previously described from Laguna del Hunco. We describe and interpret a new species of fossil Osmundaceae based on fertile and sterile pinnae. • METHODS: The fossil specimens were compared with other extant and fossil Osmundaceae based on living and herbarium material and published descriptions. A morphological matrix based on 29 characters was constructed for 17 living species in Osmundaceae, four species assigned to the fossil genus Todites, and the new fossil species. Phylogenetic analyses were conducted under parsimony using morphology and total evidence matrices. • KEY RESULTS: Both the new fossil and the Todites species were consistently resolved within the leptopteroid clade of Osmundaceae, and the new species resolved in a clade with the two living Todea species, which are now restricted to Australia, New Guinea, New Zealand, and southern Africa. • CONCLUSIONS: Todea amissa sp. nov. is the first record of Todea, living or fossil, in South America and only the second fossil record worldwide. The distribution of extant Todea on Gondwanan continents other than South America is broadly shared with other taxa from Laguna del Hunco, further indicating that a large component of this flora represents a Gondwanic biome that is no longer found on the South American continent.


Assuntos
Traqueófitas/classificação , Fósseis , Paleontologia , Filogenia , Filogeografia , Folhas de Planta/anatomia & histologia , Folhas de Planta/classificação , Folhas de Planta/genética , América do Sul , Traqueófitas/anatomia & histologia , Traqueófitas/genética
15.
Plant Cell Physiol ; 54(2): e1, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23220694

RESUMO

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.


Assuntos
Genoma de Planta , Genômica/métodos , Plantas/anatomia & histologia , Plantas/genética , Software , Alquil e Aril Transferases/genética , Bases de Dados Genéticas , Flores/genética , Internet , Anotação de Sequência Molecular , Família Multigênica , Fenótipo , Folhas de Planta/anatomia & histologia , Proteínas de Plantas/genética
16.
Am J Bot ; 99(8): 1263-75, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22847540

RESUMO

PREMISE OF THE STUDY: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. METHODS: This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). KEY RESULTS: Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. CONCLUSIONS: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.


Assuntos
Biologia Computacional/métodos , Plantas/genética , Botânica/métodos , Interpretação Estatística de Dados , Sistemas de Gerenciamento de Base de Dados , Bases de Dados Factuais , Genoma de Planta/genética , Genômica , Anotação de Sequência Molecular , Fenótipo , Plantas/anatomia & histologia , Plantas/classificação , Semântica , Terminologia como Assunto , Vocabulário Controlado
17.
Am J Bot ; 99(8): 1356-74, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22859652

RESUMO

PREMISE OF THE STUDY: Herein, we name, describe, and illustrate new macrofossil material representing Eucalyptus (Myrtaceae: Myrtoideae, Eucalypteae) from the diverse early Eocene Laguna del Hunco (LH) flora of Chubut Province, Patagonia, Argentina. We explore the significance of these fossils in light of understanding the fossil record of eucalypts and the biogeography of the Eucalypteae. METHODS: Fossils representing vegetative and reproductive organs were collected from multiple LH localities over several field seasons. These specimens were prepared, photographed, and compared to extant Eucalyptus. Additional historical collections of Patagonian fossil Eucalyptus were also examined. KEY RESULTS: Vegetative and reproductive organs representing five different Eucalyptus taxa were identified in the LH paleoflora. One new taxon each representing leaves, flower buds, and infructescences with co-occurring, isolated capsules are described and named as new Eucalyptus species. Additionally, two flower types cf. Eucalyptus, represented by one specimen each, are illustrated and briefly described. The fossil species have unique characteristics that independently suggest each belongs within the Eucalypteae. The reproductive material is most similar morphologically to extant Eucalyptus, although it also shares many similarities to the closely related genus Corymbia. CONCLUSIONS: The LH fossil Eucalyptus material is among the few eucalypt macrofossils that have recently been named and described and are the oldest macrofossils that can presently be definitively ascribed to the Eucalypteae. They also represent the only credible description of Eucalyptus fossils occurring outside of Australasia and suggest a once broader geographic distribution for this group.


Assuntos
Eucalyptus/anatomia & histologia , Fósseis , Argentina , Eucalyptus/classificação , Flores/anatomia & histologia , Flores/classificação , Geografia , Filogenia , Folhas de Planta/anatomia & histologia , Folhas de Planta/classificação
18.
Syst Biol ; 61(2): 289-313, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22201158

RESUMO

Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.


Assuntos
Fagus/genética , Fósseis , Biodiversidade , Calibragem , Classificação/métodos , DNA de Plantas/química , Fagus/classificação , Variação Genética , Filogenia , Alinhamento de Sequência , Fatores de Tempo
19.
Biology Letters ; 7: 1-4, April 27, 2011.
Artigo em Inglês | Sec. Est. Saúde SP, SESSP-IBPROD, Sec. Est. Saúde SP, SESSP-IBACERVO | ID: biblio-1060853

RESUMO

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.


Assuntos
Biologia Computacional/estatística & dados numéricos , Biologia Computacional/métodos , Paleontologia/métodos , Relógios Biológicos
20.
Biology Letters ; 7: 1-4, April 27, 2011.
Artigo em Inglês | Sec. Est. Saúde SP, SESSP-IBPROD, Sec. Est. Saúde SP, SESSP-IBACERVO | ID: ses-25310

RESUMO

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch. (AU)


Assuntos
Paleontologia/métodos , Biologia Computacional/métodos , Biologia Computacional/estatística & dados numéricos , Relógios Biológicos
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