Multi-locus phylogenetic reconstructions reveal ample reticulate relationships among genera in Anthemideae subtribe Handeliinae (Compositae)

Oberprieler, Christoph; Hassanpour, Hajar; Sonboli, Ali; Ott, Tankred; Wagner, Florian

doi:10.1007/s00606-019-01588-0

Cited by 4 publications

(8 citation statements)

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“…These two intergenic regions have been widely reported as the most divergent regions across Angiosperm lineages ( Shaw et al, 2007 ; Dong et al, 2012 ; Shaw et al, 2014 ), especially rpl32-ndhF in Asteraceae ( Timme et al, 2007 ; Salih et al, 2017 ; Zhang et al, 2017 ; Gichira et al, 2019 , Shahzadi et al, 2019 ; Zhang et al, 2019 ; Nie et al, 2020 ) and less frequently trnL-UAG-rpl32 ( Timme et al, 2007 ; Cho et al, 2019 ; Shahzadi et al, 2019 ; Shen et al, 2020 ). Numerous phylogenies in Asteraceae used trnL-UAG-rpl32 as a molecular marker (e.g., Freire et al, 2015 ; Loeuille, Keeley & Pirani, 2015 ; Loeuille et al, 2015 ; Padin, Calviño & Ezcurra, 2015 ; Soto-Trejo et al, 2015 ; Jara-Arancio, Vidal & Arroyo, 2018 ; Oberprieler et al, 2019 ), sometimes associated with ndhF-rpl32 ( Dillenberg & Kadereit, 2013 ; Steffen, Dillenberger & Kadereit, 2016 ; Gutiérrez-Larruscain et al, 2018 ; Gerschwitz-Eidt & Kadereit, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Loeuille

Thode

Siniscalchi

et al. 2021

PeerJ

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Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

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Section: Discussionmentioning

confidence: 99%

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Loeuille

Thode

Siniscalchi

et al. 2021

PeerJ

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“…One option for multilocus datasets is to infer multiple single‐gene phylogenies and make comparisons among them, by inspection (e.g. Oberprieler et al ., 2019; Kao et al ., 2020; Persson et al ., 2020). This approach has the strengths of including multiple independent lines of evidence, but lacks the inferential power of true multilocus analysis or the ability to model incomplete lineage sorting via the multispecies coalescent.…”

Section: Polyploid Phylogeneticsmentioning

confidence: 99%

Polyploid phylogenetics

Rothfels

2021

New Phytologist

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Summary Polyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy is important to long‐term evolution or is just ‘evolutionary noise’, remain unresolved due to difficulties associated with the generation and analysis of data from polyploid lineages. Many of these difficulties have been recently overcome, such that it is now often relatively straightforward to infer the full and often reticulate phylogenetic history of groups with recently formed polyploids. This nascent field of ‘polyploid phylogenetics’ allows researchers to tackle long‐standing questions of polyploid macroevolution, supplies the foundation for mechanistic models of ploidy change, and provides the opportunity to include a more complete and representative sample of plant taxa in our analyses in general.

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“…4. Owing to the lack of sequence information for all members of the outgroup and a considerable number of ingroup taxa, the Oberprieler & al. ( , 2019, Sonboli & Oberprieler (2010) and Sonboli & al.…”

Section: Species-treementioning

confidence: 99%

“…Clade support values (posterior probabilities > 0.9) are indicated. Oberprieler & al. ( , 2019, Sonboli & Oberprieler (2010) and Sonboli & al.…”

Section: Species-treementioning

confidence: 99%

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An updated subtribal classification of Compositae tribe Anthemideae based on extended phylogenetic reconstructions

et al. 2022

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Multi-locus phylogenetic reconstructions reveal ample reticulate relationships among genera in Anthemideae subtribe Handeliinae (Compositae)

Cited by 4 publications

References 38 publications

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Polyploid phylogenetics

An updated subtribal classification of Compositae tribe Anthemideae based on extended phylogenetic reconstructions

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