Phylogenetic relationships in Rosaceae inferred from chloroplast mat K and trn L- trn F nucleotide sequence data

Potter, Daniel; Gao, F.; Bortiri, P. Esteban; Oh, Sang‐Hun; Baggett, Scott

doi:10.1007/s006060200012

Cited by 116 publications

(67 citation statements)

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“…Phylogenetic relationships-In agreement with other molecular data (Bortiri et al, 2001;Potter et al, 2002), s6pdh does not support a close relationship between Prunus and Oemleria-Exochorda. On the other hand, s6pdh found the clades Oemleria-Exochorda and Sorbaria-Chamaebatiaria, which have been strongly supported by other molecular data (Morgan et al, 1994;Potter et al, 2002).…”

Section: Molecular Evolution and Utility Of S6pdh-sequences Fromsupporting

confidence: 90%

“…ITS and trnL-trnF also show branches of zero or near-zero length in this region of the tree. A similar phenomenon, i.e., short branches corresponding to the early-splitting lineages, has been observed in other groups of angiosperms (Rohwer, 2000;Fishbein et al, 2001;Potter et al, 2002) and attributed to rapid radiation. Nevertheless, s6pdh supported the same general topology as ITS and the combined ITS and trnL-trnF data sets (Lee and Wen, 2001;Bortiri et al, 2001), which will be discussed below.…”

Section: Molecular Evolution and Utility Of S6pdh-sequences Frommentioning

confidence: 61%

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The phylogenetic utility of nucleotide sequences of sorbitol 6‐phosphate dehydrogenase inPrunus(Rosaceae)

Bortiri

Gao

et al. 2002

American J of Botany

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Sequences from s6pdh, a gene that encodes sorbitol-6-phosphate dehydrogenase in the Rosaceae, are used to reconstruct the phylogeny of 22 species of Prunus. The s6pdh sequences alone and in combination with previously published sequences of the internal transcribed spacer (ITS) and the cpDNA trnL-trnF spacer are analyzed using parsimony and maximum likelihood methods. Both methods reconstructed the same phylogeny when s6pdh sequences are used alone and in combination with ITS and trnL-trnF, and the topology is in agreement with previous studies that used a larger sample size. The s6pdh sequences have about twice as many informative sites as ITS. A molecular clock is rejected for s6pdh, most likely due to greater rates of evolution in subgenera Padus and Laurocerasus than in the rest of the genus. Phylogenetic reconstruction of Prunus as determined by analysis of the combined data set suggests an early split into two clades. One is composed of subgenera Cerasus, Laurocerasus, and Padus. The second includes subgenera Amygdalus, Emplectocladus, and Prunus. Species of section Microcerasus (formerly in subgenus Cerasus) are nested within subgenus Prunus. The order of branching and relationships among early diverging lineages is weakly supported, as a result of very short branches that may indicate rapid radiation.

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Section: Molecular Evolution and Utility Of S6pdh-sequences Fromsupporting

confidence: 90%

Section: Molecular Evolution and Utility Of S6pdh-sequences Frommentioning

confidence: 61%

The phylogenetic utility of nucleotide sequences of sorbitol 6‐phosphate dehydrogenase inPrunus(Rosaceae)

Bortiri

Gao

et al. 2002

American J of Botany

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“…The topology of tribe Osmaronieae is (Exochorda þ Prinsepia) þ Oemleria (BS ! 60%; also see Lee & Wen, 2001;Potter et al, 2002). The topology of tribe Kerrieae is (…”

Section: Rosalesmentioning

confidence: 98%

Phylogeny of the Rosidae: A dense taxon sampling analysis

Sun

Naeem

et al. 2016

J of Sytematics Evolution

122

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Rosidae, a clade of approximately 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9300 species, representing 2775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non-monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large-scale analyses of the evolutionary patterns within Rosidae.Key words: phylogeny, rapid radiation, Rosidae, supermatrix.With approximately 90 000 species (estimated from Hinchliff et al., 2015), 135-140 families, and 17 orders (Soltis et al., 2005;APG III, 2009;APG IV, 2016), Rosidae contains at least one quarter of all angiosperm species and approximately 39% of eudicot species diversity (Magall on et al., 1999;Wang et al., 2009). Molecular dating indicates that Rosidae originated in the Early to Late Cretaceous, between 115 and 93 million years ago (Mya), followed by rapid diversification resulting in the Fabidae and Malvidae crown groups approximately 112 to 91 Mya (Albian to Coniacian) and 109 to 83 Mya (Cenomanian to Santonian), respectively (Wang et al., 2009;Bell et al., 2010), with major lineages diversifying in perhaps as little as 4 to 5 million years (Wang et al., 2009;Soltis et al., 2010). The radiations in Rosidae also represent the rapid rise of angiosperm-dominated forests and associated co-diversification events that have profoundly shaped much of the current terrestrial biodiversity (Wang et al., 2009).This extraordinarily diverse clade exhibits enormous heterogeneity in habitats and life forms, including herbs, shrubs, trees, vines, aquatics, succulents, and parasites. Species of Rosidae generally have bitegmic, crassinucellate ovules, distinguishing them from Asteridae, which are generally characterized by unitegmic, tenuinucellate ovules. Moreover, some members possess novel bio...

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“…with Spiraea betulifolia (AJ390368; Richardson et al, 2000), Rosa californica (AF348567; Potter et al, 2002), and Sorbaria sorbifolia (AF348569; Potter et al, 2002) as outgroups. In the analysis, all characters were equally weighted and treated as unordered.…”

Section: Haplotypementioning

confidence: 99%

Phylogeography of Spiraea alpina (Rosaceae) in the Qinghai–Tibetan Plateau inferred from chloroplast DNA sequence variations

Zhang

Gao

Zhang

et al. 2012

J of Sytematics Evolution

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The aim of the present study was to investigate the phylogeographic patterns of Spiraea alpina (Rosaceae) and clarify its response to past climatic changes in the climate-sensitive Qinghai-Tibetan Plateau (QTP). We sequenced a chloroplast DNA fragment (trnL-trnF) from 528 individuals representing 43 populations. We identified 10 haplotypes, which were tentatively divided into three groups. These haplotypes or groups were distributed in the different regions of the QTP. Only half the populations were fixed by a single haplotype, whereas the others contained two or more. In the central and eastern regions, adjacent populations at the local scale shared the same haplotype. Our phylogeographic analyses suggest that this alpine shrub survived in multiple refugia during the Last Glacial Maximum and that earlier glaciations may have trigged deep intraspecific divergences. Post-glacial expansions occurred only within populations or across multiple populations within a local range. The findings of the present study together with previous phylogeographic reports suggest that evolutionary histories of plants in the QTP are complex and variable depending on the species investigated.

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Phylogenetic relationships in Rosaceae inferred from chloroplast mat K and trn L- trn F nucleotide sequence data

Cited by 116 publications

References 0 publications

The phylogenetic utility of nucleotide sequences of sorbitol 6‐phosphate dehydrogenase inPrunus(Rosaceae)

The phylogenetic utility of nucleotide sequences of sorbitol 6‐phosphate dehydrogenase inPrunus(Rosaceae)

Phylogeny of the Rosidae: A dense taxon sampling analysis

Phylogeography of Spiraea alpina (Rosaceae) in the Qinghai–Tibetan Plateau inferred from chloroplast DNA sequence variations

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