Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)

[Display omitted] •RADseq supports a sister relationship of the orchid genera Gymnadenia and Nigritella.•Restricted gene flow between the two genera may explain discordant tree topologies.•An origin of Gymnigritella runei from extant G. conopsea and N. nigra is supported.•The separation of G. densif...

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Vydáno v:Molecular phylogenetics and evolution Ročník 136; s. 21 - 28
Hlavní autoři: Brandrud, Marie K., Paun, Ovidiu, Lorenz, Richard, Baar, Juliane, Hedrén, Mikael
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Elsevier Inc 01.07.2019
Témata:
allopolyploidy
allozymes
analytical methods
Biologi
Biological Sciences
Biological Systematics
Biologisk systematik
clearcutting
diploidy
genetic variation
genome
genomics
Geography
Gymnadenia
Gymnadenia conopsea
Likelihood Functions
loci
microsatellite repeats
Natural Sciences
Naturvetenskap
Nigritella
Orchidaceae
Orchidaceae - genetics
Phylogenomics
Phylogeny
Polyploidy
Principal Component Analysis
RADseq
Restriction Mapping
ribotypes
sequence analysis
Sequence Analysis, DNA
single nucleotide polymorphism
tetraploidy
RADseq
Polyploidy
Gymnadenia
Orchidaceae
Nigritella
Phylogenomics
ISSN:1055-7903, 1095-9513, 1095-9513
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Shrnutí:[Display omitted] •RADseq supports a sister relationship of the orchid genera Gymnadenia and Nigritella.•Restricted gene flow between the two genera may explain discordant tree topologies.•An origin of Gymnigritella runei from extant G. conopsea and N. nigra is supported.•The separation of G. densiflora from G. conopsea s.str. is supported.•Affiliation of Nigritella polyploid taxa into three distinct groups is supported. The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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content type line 23
ISSN:1055-7903
1095-9513
1095-9513
DOI:10.1016/j.ympev.2019.03.018