| 1. |
- Brandrud, Marie K., et al.
(författare)
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Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae)
- 2020
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 69:1, s. 91-109
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Tidskriftsartikel (refereegranskat)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.
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| 2. |
- Brandrud, Marie K., et al.
(författare)
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Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)
- 2019
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 136, s. 21-28
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Niegowski, Damian, 1978-, et al.
(författare)
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A simple strategy towards membrane protein purification and crystallization
- 2006
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Ingår i: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 39:1-3, s. 83-87
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Tidskriftsartikel (refereegranskat)abstract
- A simple and cost-efficient detergent screening strategy has been developed, by which a number of detergents were screened for their efficiency to extract and purify the recombinant ammonium/ammonia channel, AmtB, from Escherichia coli, hence selecting the most efficient detergents prior to large-scale protein production and crystallization. The method requires 1 ml cell culture and is a combination of immobilized metal ion affinity chromatography and filtration steps in 96-well plates. Large-scale protein purification and subsequent crystallization screening resulted in AmtB crystals diffracting to low resolution with three detergents. This strategy allows exclusion of detergents with the lowest probability in yielding protein crystals and selecting those with higher probability, hence, reducing the number of detergents to be screened prior to large-scale membrane protein purification and perhaps also crystallization.
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| 4. |
- Widen, Björn, et al.
(författare)
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Evolution in Helianthemum oelandicum (Cistaceae)-evidence of Holocene differentiation in morphology on the Baltic island of Öland, south-eastern Sweden
- 2023
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Ingår i: Botanical Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 202:2, s. 270-293
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Tidskriftsartikel (refereegranskat)abstract
- We use Helianthemum oelandicum subsp. oelandicum as a model for studies of mechanisms shaping the diversity in a rapidly radiating lineage of the H. oelandicum aggregate. Locally, correlations between drainage conditions (using GIS to measure variation in the micro-Topography on the more or less horizontal bedrock) and frequency of alleles of Mendelian genes for pubescence indicated that hairs are markers of adaptation to the unique environmental conditions (drought and periodic flooding) on the alvar habitats of Öland. An allozyme study showed that 1 and 4% of the genetic diversity is partitioned among two varieties and natural populations, respectively. FST for hair alleles was up to ten time greater than FST for allozymes. Öland rose above sea level after the LGM, which makes it possible to date the onset of the post-glacial diversification on the island. Only two, mainly allopatric, plastid DNA haplotypes were detected, H1 and H2. The southern Helianthemum oelandicum subsp. oelandicum var. canescens has only H1, whereas the more widespread var. oelandicum possesses both haplotypes. A restricted occurrence of haplotype H1 in the core area of var. oelandicum in the central Öland, coincided with the highest elevation on the island, probably representing the post-glacial arrival of the species on the island.
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