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Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae)

Brandrud, Marie K.; Baar, Juliane; Lorenzo, Maria Teresa; Athanasiadis, Alexander; Bateman, Richard M.; Chase, Mark W.; Hedrén, Mikael LU and Paun, Ovidiu (2019) In Systematic Biology
Abstract
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum... (More)
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, non-model, polyploid plant complexes. (Less)
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organization
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type
Contribution to journal
publication status
in press
subject
in
Systematic Biology
publisher
Oxford University Press
ISSN
1063-5157
DOI
10.1093/sysbio/syz035
language
English
LU publication?
yes
id
1e2d303a-6bc1-4fb7-93ea-66f925b938bb
date added to LUP
2019-05-23 12:59:28
date last changed
2019-05-28 17:58:25
@article{1e2d303a-6bc1-4fb7-93ea-66f925b938bb,
  abstract     = {Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, non-model, polyploid plant complexes.},
  articleno    = {syz035},
  author       = {Brandrud, Marie K. and Baar, Juliane and Lorenzo, Maria Teresa and  Athanasiadis, Alexander and Bateman, Richard M. and Chase, Mark W. and Hedrén, Mikael and Paun, Ovidiu},
  issn         = {1063-5157},
  language     = {eng},
  publisher    = {Oxford University Press},
  series       = {Systematic Biology},
  title        = {Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae)},
  url          = {http://dx.doi.org/10.1093/sysbio/syz035},
  year         = {2019},
}