dc.contributor.author
Escobari, Belen
dc.contributor.author
Borsch, Thomas
dc.contributor.author
Quedensley, Taylor S.
dc.contributor.author
Gruenstaeudl, Michael
dc.date.accessioned
2021-11-30T14:07:29Z
dc.date.available
2021-11-30T14:07:29Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/32920
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-32646
dc.description.abstract
Premise
The genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it.
Methods
We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference.
Results
Our results indicate that the inclusion of all plastid genome partitions is needed to infer well-supported phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia.
Conclusions
The concatenation and combined analysis of all plastid genome partitions and the construction of manually-curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of well-supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.
en
dc.format.extent
22 Seiten
dc.rights.uri
https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject
chloroplast genome
en
dc.subject
manual sequence alignment
en
dc.subject
noncoding DNA
en
dc.subject
phylogenetic inference
en
dc.subject
sequence partitioning
en
dc.subject
South America
en
dc.subject.ddc
500 Naturwissenschaften und Mathematik::580 Pflanzen (Botanik)::580 Pflanzen (Botanik)
dc.title
Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation.doi
10.1002/ajb2.1775
dcterms.bibliographicCitation.journaltitle
American Journal of Botany
dcterms.bibliographicCitation.number
11
dcterms.bibliographicCitation.pagestart
2235
dcterms.bibliographicCitation.pageend
2256
dcterms.bibliographicCitation.volume
108
dcterms.bibliographicCitation.url
https://doi.org/10.1002/ajb2.1775
refubium.affiliation
Biologie, Chemie, Pharmazie
refubium.affiliation
Botanischer Garten und Botanisches Museum Berlin-Dahlem (BGBM)
refubium.affiliation.other
Institut für Biologie
refubium.funding
DEAL Wiley
refubium.note.author
Die Publikation wurde aus Open Access Publikationsgeldern der Freien Universität Berlin gefördert.
refubium.resourceType.isindependentpub
no
dcterms.accessRights.openaire
open access
dcterms.isPartOf.eissn
1537-2197