| 1. |
- Backlund, Maria, 1969-
(författare)
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Phylogenetic Studies in the Gentianales – Approaches at Different Taxonomic Levels
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis deals with phylogenetic relationships at different taxonomic levels. All the plants studied are or have been included in the order Gentianales, which comprises about 17 200 species. The phylogenies are based on parsimony analyses of nucleotide sequence data (DNA) from different regions in the chloroplast genome, but morphological characteristics have also been studied. Analyses of sequence data from the genes rbcL and ndhF provide the interfamilial structure of the order Gentianales, shown to comprise the families Apocynaceae (incl. Asclepiadaceae), Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae. Exclusion of certain genera from the Loganiaceae is confirmed and their phylogenetic positions are clarified. Some of these genera remain within the Gentianales, while others belong to other orders. Exclusion of the tribe Buddlejeae from the Loganiaceae is confirmed, and a monophyletic group formed by Buddleja, Emorya, Gomphostigma, and Nicodemia is recognized and placed in the Lamiales. The Loganiaceae s.str. forms, after these exclusions, a strongly supported monophyletic group comprising 13 genera. The tribe Paederieae in the family Rubiaceae is analysed using sequence data from the regions rbcL gene, rps16 intron, and the regions trnT-F, and is shown to be paraphyletic. These results lead to a new circumscription of Paederieae comprising the genera Leptodermis, Paederia, Serissa, and Spermadictyon. The tribe Putorieae is reestablished with the single genus Plocama, including 34 species. Aitchisonia, Choulettia, Crocyllis, Gaillonia, Jaubertia, Pseudogaillonia, Pterogaillonia, and Putoria are reduced to synonyms of Plocama based on the molecular analyses and morphological studies. The Mediterranean species of the re-circumscribed Plocama, previously segregated as the genus Putoria, are revised. Two species, Plocama calabrica and P. brevifolia, are recognized, their synonymics are established, and seven lectotypes are selected.
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| 2. |
- Balao, Francisco, et al.
(författare)
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Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima
- 2017
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083. ; 26:14, s. 3649-3662
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Tidskriftsartikel (refereegranskat)abstract
- The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post-transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA-dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.
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| 3. |
- Balao, F, et al.
(författare)
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Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex.
- 2015
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 1365-2540 .- 0018-067X.
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Tidskriftsartikel (refereegranskat)abstract
- Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.Heredity advance online publication, 25 November 2015; doi:10.1038/hdy.2015.98.
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| 4. |
- 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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| 5. |
- 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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| 6. |
- Eriksson, Mimmi C., et al.
(författare)
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Repeat Dynamics across Timescales : A Perspective from Sibling Allotetraploid Marsh Orchids (Dactylorhiza majalis s.l.)
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:8
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Tidskriftsartikel (refereegranskat)abstract
- To provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridization between diploids D. fuchsii and D. incarnata. Our results first reveal that the paternal D. incarnata genome shows a marked increased content of LTR retrotransposons compared to the maternal species, reflected in its larger genome size and consistent with a previously hypothesized bottleneck. With regard to the allopolyploids, in the youngest D. purpurella both genome size and TE composition appear to be largely additive with respect to parents, whereas for polyploids of intermediate ages we uncover rampant genome expansion on a magnitude of multiple entire genomes of some plants such as Arabidopsis. The oldest allopolyploids in the series are not larger than the intermediate ones. A putative tandem repeat, potentially derived from a non-autonomous miniature inverted-repeat TE (MITE) drives much of the genome dynamics in the allopolyploids. The highly dynamic MITE-like element is found in higher proportions in the maternal diploid, D. fuchsii, but is observed to increase in copy number in both subgenomes of the allopolyploids. Altogether, the fate of repeats appears strongly regulated and therefore predictable across multiple independent allopolyploidization events in this system. Apart from the MITE-like element, we consistently document a mild genomic shock following the allopolyploidizations investigated here, which may be linked to their relatively large genome sizes, possibly associated with strong selection against further genome expansions.
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| 7. |
- Hedrén, Mikael, et al.
(författare)
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A replacement name for a species of Hypoestes (Acanthaceae) from Somalia
- 2015
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Ingår i: Willdenowia. - : Botanic Garden and Botanical Museum Berlin, Freie Universitaet Berlin. - 0511-9618 .- 1868-6397. ; 45:1, s. 93-93
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Tidskriftsartikel (refereegranskat)abstract
- Hypoestes canescens Hedren & Thulin, nom. nov., is proposed for the illegitimate name H. cinerea Hedren, non C. B. Clarke.
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| 8. |
- Hedrén, Mikael, et al.
(författare)
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Acanthaceae
- 2006
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Ingår i: Flora of Somalia, vol 3. - 1 84246 099 4 ; 3, s. 374-454
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Somalian vegetation is rich and varied, and covers one of the most arid regions of Africa. Volume 3 completes the angiosperms, and includes an index to all of the genera described in the four volumes.
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| 9. |
- Hedrén, Mikael, et al.
(författare)
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Amplified fragment length polymorphisms (AFLP) reveal details of polyploid evolution in Dactylorhiza (Orchidaceae)
- 2001
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Ingår i: American Journal of Botany. - 0002-9122. ; 88:10, s. 1868-1880
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Tidskriftsartikel (refereegranskat)abstract
- The utility of the PCR-based AFLP technique (polymerase chain reactions amplified fragment length polymorphisms) was explored in elucidating details of polyploid evolution in the Eurasian orchid genus Dactylorhiza. We emphasized Swedish taxa but also included some material from the British Isles and elsewhere in Europe. Three different sets of primers, amplifying different subsets of restriction fragments, independently revealed similar patterns for relationships among the Dactylorhiza samples investigated. The AFLP data support the general picture of polyploid evolution in Dactylorhiza, i.e., that allotetraploid derivatives have arisen repeatedly as a result of hybridization beween the two parental groups D. incarnata s.l. (sensu lato; diploid marsh orchids) and the D. maculata group (spotted orchids), Within the incarnata s.l. group. morphologically defined varieties were interdigitated. The D. maculata group consisted of two distinct subgroups, one containing autotetraploid D. maculata subsp. maculata and the other containing diploid D. maculata subsp. fuchsii. Allotetraploids showed a high degree of additivity for the putative parental genomes, and relationships among them were partly correlated to morphologically based entities. but also to geographic distribution. Thus, allotetraploid taxa from the British Isles clustered together, rather than with morphologically similar plants from other areas.
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| 10. |
- Hedrén, Mikael, et al.
(författare)
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Asymmetric contributions of seed and pollen to gene dispersal in the marsh orchid Dactylorhiza umbrosa in Asia Minor
- 2021
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:8, s. 1791-1805
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Tidskriftsartikel (refereegranskat)abstract
- Orchids differ from other plants in their extremely small and partly air-filled seeds that can be transported long distances by wind. Seed dispersal in orchids is expected to contribute strongly to overall gene flow, and orchids generally express low levels of genetic differentiation between populations and low pollen to seed flow ratios. However, studies in orchids distributed in northern Europe have often found a poor geographic structuring of genetic variation. Here, we studied geographic differentiation in the marsh orchid Dactylorhiza umbrosa, which is widely distributed in upland regions from Asia Minor to Central Asia. These areas were less affected by Pleistocene ice ages than northern Europe and the orchid should have been able to survive the last ice age in local refugia. In the plastid genome, which is dispersed by seeds, populations at close distance were clearly divergent, but the differentiation still increased with geographic distance, and a significant phylogeographic structure had developed. In the nuclear genome, which is dispersed by both seeds and pollen, populations showed an even stronger correlation between genetic and geographic distance, but average levels of differentiation were lower than in the plastid genome, and no phylogeographic structure was evident. Combining plastid and nuclear data, we found that the ratio of pollen to seed dispersal (mp/ms) decreases with physical distance. Comparison with orchids that grow in parts of Europe that were glaciated during the last ice suggests that a balanced structure of genetic diversity develops only slowly in many terrestrial orchids, despite efficient seed dispersal.
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