Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae)

Johnson, Leigh A.; Chan, Lauren M.; Weese, Terri L.; Busby, Lisa D.; McMurry, Samuel

doi:10.1016/j.ympev.2008.05.036

Cited by 25 publications

(24 citation statements)

References 69 publications

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“…For example, Gielly and Taberlet (1994) showed that introns and intergenic spacers evolve 1.93-11.72 times faster than rbcL and that indels occur as often as nucleotide substitutions. Thus, different chloroplast sites can also result in a different phylogenetic status of plant species because they have different evolutionary rates (Freeland 2005;Johnson et al 2008).…”

Section: Discussionmentioning

confidence: 99%

What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

Yang

Wang

et al. 2010

Plant Biosystems - An International Journal Dealing with all As

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DNA sequence data have been widely used to evaluate species delimitations and examine infraspecific relationships. However, species placements inferred from different nucleotide sequences are frequently in conflict. As an example of plant species placement based on nucleotide sequences, the phylogenetic placement of Dipteronia dyerana Henry (Aceraceae) was analyzed in the present study. The study species included eight Acer species (from different sections of Acer ), two Dipteronia species, and two outgroup taxa. Phylogenetic trees based on five datasets ( ITS , trnL-F , trnD-trnT , psbM-trnD , and rpl16 regions) as well as their combined datasets were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Further analyses were conducted to compare the strict consensus trees based on single regions and the combination of different regions. The results revealed a significant discrepancy among the phylogenetic placements of D. dyerana , inferred from various sequences. Phylogenetic trees using MP analysis based on trnD-trnT , rpl16 , and the four chloroplast combined sequences supported the genus Dipteronia as a monophyletic group, while in the other trees D. dyerana was positioned either in parallel with D. sinensis and Acer species or within the genus Acer . In ML analysis, only rpl16 and the four chloroplast combined sequence datasets supported the genus Dipteronia as a monophyletic group. We concluded that, although significant genetic differentiation occurred between D. dyerana and D. sinensis , D. dyerana was more advanced than D. sinensis . However, whether Dipteronia is monophyletic remains to be further investigated, e.g., by using more closely related taxa and more sequences. Furthermore, in addition to internal transcribed spacer sequences, more chloroplast gene sequences should be used for phylogenetic analyses of species.

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Section: Discussionmentioning

confidence: 99%

What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

Yang

Wang

et al. 2010

Plant Biosystems - An International Journal Dealing with all As

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“…Although not present in all species (e.g. Eriastrum eremicum, figure 6g; P. divaricata; Schö nenberger 2009), connective protrusions seem particularly well developed in taxa belonging to early diverging lineages of the family (for phylogenetic relationship within Polemoniaceae, see Johnson et al 2008) such as A. gloriosa (figure 6h) and C. coerulea (figure 6j ) (Schö nenberger 2009). Again, this is particularly interesting, because conspicuous connective protrusions are characteristics of the sister family Fouquieriaceae (Henrickson 1972;Schö nenberger 2009).…”

Section: Phlox Divaricata)mentioning

confidence: 99%

Diversity and evolution of floral structure among early diverging lineages in the Ericales

Schönenberger

Balthazar

Sytsma

2010

Phil. Trans. R. Soc. B

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This is a combination of review and original data on floral structure and diversity in the two earliest diverging lineages of the Ericales, i.e. the balsaminoids, comprising Balsaminaceae, Marcgraviaceae and Tetrameristaceae, and the polemonioids, comprising Fouquieriaceae and Polemoniaceae. Each clade is strongly supported in molecular studies, while structural synapomorphies have largely been lacking. For the balsaminoid families, we compare floral morphology, anatomy and histology among selected taxa and find that the entire clade is strongly supported by the shared presence of nectariferous tissue in the floral periphery, thread-like structures on anthers, truncate stigmas, secretion in the ovary, as well as mucilage cells, raphides and tannins in floral tissues. A possible sister group relationship between Balsaminaceae and Tetrameristaceae is supported by the shared presence of post-genital fusion of filaments and ovary and a star-shaped stylar canal. For polemonioids, we document unexpected diversity of floral features in Polemoniaceae, partly providing structural links to Fouquieriaceae. Features include cochlear and quincuncial corolla aestivation, connective protrusions, ventrifixed anthers and nectariferous tissue in the base of the ovary. In addition, we outline future directions for research on floral structure in the Ericales and briefly discuss the general importance of structural studies for our understanding of plant phylogeny and evolution.

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“…We isolated DNA and PCR amplified the nuclear ribosomal ITS1, 5.8s, and ITS2 region (White et al 1990, Porter 1996, the plastid 5' trnK intron and 5' portion of matK (Johnson & Solits 1995, Johnson & Johnson 2006, trnL-trnL-trnF intergenic spacer and intron (Taberlet et al 1991), trnS-trnG intergenic spacer (Hamilton 1999), and rpl16 regions (Small et al 1998). Our methods for amplification and sequencing follow Johnson et al (2008), and we deposited the DNA sequences in Genbank (accession numbers KX017843-KX017976; HQ116860, HQ116865, HQ116961, HQ116966, HQ117005, HQ117011, HQ117046, HQ117051, HQ117085, HQ117090). We aligned sequences by eye using AliView (Larsson 2014) and coded indels as present or absent using simple indel coding (Simmons & Ochoterena 2000) as implemented in SeqState (Muller 2005).…”

Section: Methodsmentioning

confidence: 99%

Navarretia crystallina and N. miwukensis (Polemoniaceae): new species endemic to California with affinity for soils derived from pyroclastic deposits

Johnson

Gowen²,

Johnson

et al. 2016

Phytotaxa

Self Cite

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Two species endemic to California in the western United States, Navarretia crystallina and N. miwukensis, are here described. Both species occur on soils derived from pyroclastic flows. N. crystallina is distributed more widely, generally at higher elevations, and occurs predominantly to the north and east of N. miwukensis. Though similar in habit to N. divaricata and N. prolifera, N. crystallina and N. miwukensis can be distinguished consistently from both of these species by inflorescence structure, bract lobing, and flower size, and from each other by bract and calyx lobe shape, inflorescence indumentum, and stamen insertion. The species are also distinguishable by DNA sequences.

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Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae)

Cited by 25 publications

References 69 publications

What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

Diversity and evolution of floral structure among early diverging lineages in the Ericales

Navarretia crystallina and N. miwukensis (Polemoniaceae): new species endemic to California with affinity for soils derived from pyroclastic deposits

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