Show simple item record

Title

Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment

dc.contributor.authorWanke, Stefan
dc.contributor.authorGranados Mendoza, Carolina
dc.contributor.authorMueller, Sebastian
dc.contributor.authorPaizanni Guillen, Anna
dc.contributor.authorNeinhuis, Christoph
dc.contributor.authorLemmon, Alan R.
dc.contributor.authorLemmon, Emily Moriarty
dc.contributor.authorSamain, Marie-Stephanie
dc.date.accessioned2019-08-09T22:22:50Z
dc.date.available2019-08-09T22:22:50Z
dc.date.issued2017
dc.identifier.citationStefan Wanke, Carolina Granados Mendoza, Sebastian Müller, Anna Paizanni Guillén, Christoph Neinhuis, Alan R. Lemmon, Emily Moriarty Lemmon, Marie-Stéphanie Samain, Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment, Molecular Phylogenetics and Evolution, Volume 117, 2017, Pages 111-123.
dc.identifier.urihttp://hdl.handle.net/11627/5050
dc.description.abstract"Recalcitrant relationships are characterized by very short internodes that can be found among shallow and deep phylogenetic scales all over the tree of life. Adding large amounts of presumably informative sequences, while decreasing systematic error, has been suggested as a possible approach to increase phylogenetic resolution. The development of enrichment strategies, coupled with next generation sequencing, resulted in a cost-effective way to facilitate the reconstruction of recalcitrant relationships. By applying the anchored hybrid enrichment (AHE) genome partitioning strategy to Aristolochia using an universal angiosperm probe set, we obtained 231–233 out of 517 single or low copy nuclear loci originally contained in the enrichment kit, resulting in a total alignment length of 154,756 bp to 160,150 bp. Since Aristolochia (Piperales; magnoliids) is distantly related to any angiosperm species whose genome has been used for the plant AHE probe design (Amborella trichopoda being the closest), it serves as a proof of universality for this probe set. Aristolochia comprises approximately 500 species grouped in several clades (OTUs), whose relationships to each other are partially unknown. Previous phylogenetic studies have shown that these lineages branched deep in time and in quick succession, seen as short-deep internodes. Short-shallow internodes are also characteristic of some Aristolochia lineages such as Aristolochia subsection Pentandrae, a clade of presumably recent diversification. This subsection is here included to test the performance of AHE at species level. Filtering and subsampling loci using the phylogenetic informativeness method resolves several recalcitrant phylogenetic relationships within Aristolochia. By assuming different ploidy levels during bioinformatics processing of raw data, first hints are obtained that polyploidization contributed to the evolution of Aristolochia. Phylogenetic results are discussed in the light of current systematics and morphology."
dc.publisherElsevier
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internacional
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectEnrichment strategy
dc.subjectNext generation sequencing
dc.subjectPhylogenomics
dc.subjectPolyploidy
dc.subjectShort internodes
dc.subjectRecent diversification
dc.subjectUniversal nuclear probe set
dc.subject.classificationBIOLOGÍA MOLECULAR
dc.titleRecalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment
dc.typearticle
dc.identifier.doihttps://doi.org/10.1016/j.ympev.2017.05.014
dc.rights.accessAcceso Abierto


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

Attribution-NonCommercial-NoDerivatives 4.0 Internacional
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 Internacional