Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences

Soltis, Douglas E.; Soltis, Pamela S.; Chase, Mark W.; Mort, Mark E.; Albach, Dirk C.; Zanis, Michael J.; Savolainen, Vincent; HAHN, WILLIAM H.; Hoot, Sara B.; Fay, Michael F.; AXTELL, MICHAEL; Swensen, Susan M.; Prince, Linda M.; Kress, W. John; Nixon, Kevin C.; Farris, James S.

doi:10.1111/j.1095-8339.2000.tb01588.x

Cited by 905 publications

(650 citation statements)

References 100 publications

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“…The relationships among Vitaceae are indistinct in angiosperms, and the family does not appear to have any close relatives to other families of rosids (Soltis et al, 2000). In the Cronquist system, the Vitaceae family was placed near Rhamnaceae (Cronquist, 1988).…”

Section: Introductionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Raman

Park

2016

Front. Plant Sci.

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Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of the plant Ampelopsis.

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Section: Introductionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Raman

Park

2016

Front. Plant Sci.

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“…Placement of Caryophyllales has been controversial, and phylogenetic analyses of single or multiple gene sequences have not been able to resolve their relationship to rosids or asterids (7,33). Phylogenetic estimates based on 61 plastid protein-coding genes supported a sister relationship between Caryophyllales and asterids (5,15,16), although taxon sampling was limited in these studies.…”

Section: Mack Et Al (5) Used 61 Genes and 24 Genomes And Mp Trees Pmentioning

confidence: 81%

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

Jansen

Cai

Raubeson

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

1,002

1,048

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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. angiosperm evolution ͉ molecular evolution A ngiosperms, the largest clade of land plants with Ͼ250,000 species, experienced rapid radiation soon after their first appearance in the fossil record (1). As a result, flowering plants exhibit incredible diversity in habit, morphology, anatomy, physiology, and reproductive biology. This variation has presented major challenges to biologists interested in the origin and evolution of these traits, and resolving these issues critically depends on having a well resolved and strongly supported phylogenetic framework. Over the past 20 years, numerous phylogenetic studies have used both morphological and molecular data to assess relationships among the major clades (reviewed in ref.2), resulting in a widely accepted classification of angiosperms with 45 orders and 457 families (3).For nearly two decades, most phylogenetic analyses of angiosperms have relied on DNA sequences of one to several genes from the plastid, mitochondrial, and nuclear genomes (reviewed in ref.2). Despite these intensive efforts there are still uncertainties regarding relationships among several major clades throughout angiosperms, including the earliest diverging lineages. Recent studies support the placement of Amborella sister to all remaining angiosperms, but support is often low. Amborella has also been placed with waterlilies (Nymphaeales) in a clade sister to other angiosperms (4-7). In many studies, resolution of r...

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“…One of the most diverse and abundant families in the London Clay flora, the Icacinaceae are represented by at least seven genera and 27 species, according to the original works of Reid and Chandler (1933) and Chandler (1961Chandler ( , 1964Chandler ( , 1978. The family, in the traditional sense (Engler 1893;Howard 1940;Sleumer 1942), was grossly polyphyletic (Soltis et al 2000;Kårehed 2001), but recent phylogenetic work has greatly clarified the composition of the family and relationships within it (Byng et al 2014;Stull et al 2015). Furthermore, recent and ongoing studies of fruit morphology have highlighted characters useful for diagnosing clades within the family (e.g., Stull et al 2011Allen et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Revision of Icacinaceae from the Early Eocene London Clay flora based on X-ray micro-CT

Stull

Adams

Manchester

et al. 2016

Botany

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Abstract:The Early Eocene (Ypresian) London Clay Formation contains one of the most important fruit and seed assemblages from the Paleogene, including a large diversity of taxa (>350 spp.) preserved as pyrite permineralizations retaining 3D structure as well as anatomical detail. Despite the importance of the flora for understanding angiosperm biogeographic and evolutionary history, the majority of the fossil material has not been revisited since the original taxonomic treatments by E.M. Reid and M.E.J. Chandler. Given subsequent advances in our understanding of angiosperm phylogeny and fruit morphology, coupled with technological advances in imaging/visualizing fossil material, many of the taxa represented in the flora deserve further study. Here we present a revision of the pantropical family Icacinaceae using X-ray micro-computed tomography (micro-CT) images of 21 species from the flora. Based on the results, four new combinations are made, a new fossil-genus is established for a distinctive species with affinities to the Phytocreneae, and emended diagnoses are provided for eight taxa. Of the seven genera recognized from the flora, only one, Iodes Blume, is extant. This study offers important insights on the biogeographic and evolutionary history of Icacinaceae, which is one of the most abundant and diverse components of the flora from the London Clay Formation.Key words: endocarps, Eocene, Icacinaceae, Iodes, London Clay, X-ray tomography.Résumé : La formation d'argile de Londres (London Clay Formation) de l'Éocène précoce (Yprésien) comprend un des assemblages de fruits et de graines du Paléogène le plus important, comprenant une grande diversité de taxons (>350 spp.) préservés sous forme de minéralisations de pyrite qui conservent la structure en 3D de même que le détail anatomique. Malgré l'importance de la flore pour comprendre l'histoire biogéographique et évolutive des angiospermes, la majorité du matériel fossile n'a pas été revisité depuis les descriptions taxonomiques originales de E.M. Reid et M.E.J. Chandler. Compte tenu des progrès subséquents quant à notre compréhension de la phylogénie des angiospermes et de la morphologie des fruits, couplés aux progrès technologiques en imagerie/ visualisation du matériel fossile, plusieurs taxons représentés dans la flore méritent d'être étudiés davantage. Les auteurs présentent ici une révision de la famille pantropicale des Icacinaceae à l'aide d'images en microtomographie aux rayons-X assistée par ordinateur (micro-CT) de 21 espèces de la flore. Selon les résultats, quatre nouvelles combinaisons sont faites, un nouveau genre fossile est établi pour une espèce distinctive ayant des affinités avec les Phytocreneae, et des diagnostics amendés sont fournis pour huit taxons. Des sept genres reconnus de la flore, un seul, Iodes Blume existe toujours. Cette étude offre un important aperçu de l'histoire biogéographique et évolutive des Icacinaceae, qui constituent une des composantes les plus abondantes et diverses de la flore de la formation de l'argile de Londr...

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Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences

Cited by 905 publications

References 100 publications

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

Revision of Icacinaceae from the Early Eocene London Clay flora based on X-ray micro-CT

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