Chloroplast capture and intra- and inter-continental biogeographic diversification in the Asian – New World disjunct plant genus Osmorhiza (Apiaceae)

Yi, Ting‐Shuang; Jin, Guihua; Wen, Jun

doi:10.1016/j.ympev.2014.09.028

Cited by 67 publications

(43 citation statements)

References 100 publications

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“…In addition, these studies have shown an incongruence between plastid and nuclear phylogenies 4, 12, 16 . A similar incongruence has been reported in recent studies of the genus Oryza 17 , the tribe Arundinarieae 18 , the genera Medicago 19 and Ilex 20 and has been attributed to the use of markers with insufficient phylogenetic signals, incomplete lineage sorting, or complex evolutionary issues. Moreover, the selected loci unfortunately have not provided sufficient phylogenetic resolution at the species level for Lilium .…”

Section: Introductionsupporting

confidence: 68%

Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

Yang

et al. 2017

Sci Rep

115

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Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this study, we present the use of complete chloroplast genomes to explore the phylogeny of this genus. We sequenced nine Lilium chloroplast genomes and retrieved seven published chloroplast genomes for comparative and phylogenetic analyses. The genomes ranged from 151,655 bp to 153,235 bp in length and had a typical quadripartite structure with a conserved genome arrangement and moderate divergence. A comparison of sixteen Lilium chloroplast genomes revealed ten mutation hotspots. Single nucleotide polymorphisms (SNPs) for any two Lilium chloroplast genomes ranged from 8 to 1,178 and provided robust data for phylogeny. Except for some of the shortest internodes, phylogenetic relationships of the Lilium species inferred from the chloroplast genome obtained high support, indicating that chloroplast genome data will be useful to help resolve the deeper branches of phylogeny.

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Section: Introductionsupporting

confidence: 68%

Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

Yang

et al. 2017

Sci Rep

115

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“…Alternatively, it may be an analytical artefact resulting from lack of phylogenetic signal, i.e., missing data and possible sampling error of characters, taxa, or both (Salichos & al., 2014, and references therein). Discrepancy between cpDNA and nrDNA ITS data has been reported in several studies of Apiaceae (e.g., Lee & Downie, 2006;Spalik & al., 2009;Zhou & al., 2009;Bone & al., 2011;Yi & al., 2015). In this study, 13 accessions Fig.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny of Apiaceae subtribe Daucinae and the taxonomic delineation of its genera

Banasiak

Wojewódzka

Baczyński

et al. 2016

TAXON

103

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Scandiceae subtribe Daucinae encompasses umbellifers that have fruits with prominent secondary ridges projecting into wings (former tribe Laserpitieae) or spines (former tribe Caucalideae pro parte). It comprises several economically or medicinally important genera including Cuminum, Daucus, Laser, Laserpitium and Thapsia among others. Recent molecular studies, based mostly on nrDNA ITS sequences, revealed that neither Daucus nor Laserpitium are monophyletic. To address issues of relationships and apply respective nomenclatural changes, we obtained additional ITS sequences as well as independent data from three plastid markers—rps16 intron, rpoC1 intron and rpoB‐trnC intergenic spacer—for a comprehensive sample of the subtribe. We examined data for 260 accessions representing all genera of Daucinae and 81 of its ca. 93 species. Phylogenetic trees were estimated using maximum likelihood and Bayesian inference methods. The results indicate that former Laserpitieae constitute a paraphyletic grade at the base of the spiny‐fruited members of Daucinae while traditionally delimited Daucus and Laserpitium are polyphyletic. To maintain a monophyletic Daucus, we suggest including the following genera and species into its synonymy: Agrocharis, Melanoselinum, Monizia, Pachyctenium, Pseudorlaya, Rouya, Tornabenea, Athamanta dellacellae and Cryptotaenia elegans. The species of Laserpitium occur in seven clades and only six species of the Laserpitium s.str. clade retain the generic name. Several species are transferred to Ekimia, Laser and Thapsia; additionally, a monospecific genus Siler is restored and a new genus, Silphiodaucus, is established. The inclusion of Ammodaucus into Thapsia suggested in an earlier study is not supported. The position of Laserpitium pseudomeum requires further study.

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“…Both relationships were well-supported. Various mechanisms have been proposed to explain discordant topologies between gene trees, such as allopolyploidy, hybridization, horizontal gene transfer, incomplete lineage sorting (ILS), different rate of molecular evolution, and chloroplast capture (Degtjareva et al 2012; García et al 2014; Yi et al 2015). …”

Section: Discussionmentioning

confidence: 99%

A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations

Duan¹,

Yang²,

Liu³

et al. 2016

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Based on sequence data of nuclear ITS and plastid matK, trnL-F and psbA-trnH markers, the phylogeny of the subtribes Caraganinae and Chesneyinae in tribe Caraganeae was inferred. The results support the monophyly of each of the subtribes. Within subtribes Caraganinae, Calophaca and Halimodendron are herein transferred into Caragana to ensure its generic monophyly. The subtribe Chesneyinae is composed of four well-supported genera: Chesneya, Chesniella, Gueldenstaedtia and Tibetia. Based on phylogenetic, morphological, distributional and habitat type evidence, the genus Chesneya was divided into three monophyletic sections: Chesneya sect. Chesneya, Chesneya sect. Pulvinatae and Chesneya sect. Spinosae. Chesneya macrantha is herein transferred into Chesniella. Spongiocarpella is polyphyletic and its generic rank is not maintained. The position of Chesneya was incongruent in the nuclear ITS and the plastid trees. A paternal chloroplast capture event via introgression is hypothesized for the origin of Chesneya, which is postulated to have involved the common ancestor of Chesniella (♂) and that of the Gueldenstaedtia – Tibetia (GUT) clade (♀) as the parents.

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Chloroplast capture and intra- and inter-continental biogeographic diversification in the Asian – New World disjunct plant genus Osmorhiza (Apiaceae)

Cited by 67 publications

References 100 publications

Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

Phylogeny of Apiaceae subtribe Daucinae and the taxonomic delineation of its genera

A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations

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