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Mikael Hedrén - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae)
Systematic biology, 2019Co-Authors: Marie K. Brandrud, Mikael Hedrén, Mark W. Chase, Richard M. Bateman, Juliane Baar, Maria Teresa Lorenzo, Alexander Athanasiadis, Ovidiu PaunAbstract: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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Hva er Dactylorhiza traunsteineri
Blyttia, 2018Co-Authors: Mikael Hedrén, Steinar SkredeAbstract:Comments are given on the identity of some populations of allotetraploid Dactylorhiza in southern Norway and their relationships to populations elsewhere in Scandinavia and in continental Europe. The most widespread allotetraploid member of Dactylorhiza in southern Norway is D. majalis ssp. sphagnicola. This subspecies is confined to poor and medium-rich fens dominated by peat mosses, Sphagnum, in the bottom layer. Subspecies sphagnicola has sometimes been included in D. traunsteineri, which is another allotetraploid member of Dactylorhiza described from Austria, but molecular analyses show that these taxa are distinct. Subspecies sphagnicola is distributed from northern France, Belgium and western Germany to Central Scandinavia, but it does not grow on Gotland or to the east of the Baltic Sea. D. majalis ssp. lapponica is only sparsely represented in southern Norway, but is known from at least one site in Lier southwest of Oslo. This subspecies grows in rich fens with high pH. It is also rare on the southern Swedish mainland, but is common on Gotland and is widespread in regions with calcareous bedrock in mid and northern Scandinavia. Mountain populations are often low-grown, have leaves with spotted upper surface, and have anthocyanine-rich stems and flowers. D. majalis ssp. lapponica is related to the Central European D. traunsteineri, but the epithet “lapponica” has priority over “traunsteineri” at subspecies level. (Less)
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Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza
Scientific reports, 2016Co-Authors: Hans Jacquemyn, Daniel Tyteca, Mikael Hedrén, Michael Waud, Vincent S. F. T. Merckx, Rein Brys, Bart LievensAbstract:Orchid species are critically dependent on mycorrhizal fungi for completion of their life cycle, particularly during the early stages of their development when nutritional resources are scarce. As such, orchid mycorrhizal fungi play an important role in the population dynamics, abundance, and spatial distribution of orchid species. However, less is known about the ecology and distribution of orchid mycorrhizal fungi. In this study, we used 454 amplicon pyrosequencing to investigate ecological and geographic variation in mycorrhizal associations in fourteen species of the orchid genus Dactylorhiza. More specifically, we tested the hypothesis that variation in orchid mycorrhizal communities resulted primarily from differences in habitat conditions where the species were growing. The results showed that all investigated Dactylorhiza species associated with a large number of fungal OTUs, the majority belonging to the Tulasnellaceae, Ceratobasidiaceae and Sebacinales. Mycorrhizal specificity was low, but significant variation in mycorrhizal community composition was observed between species inhabiting different ecological habitats. Although several fungi had a broad geographic distribution, Species Indicator Analysis revealed some fungi that were characteristic for specific habitats. Overall, these results indicate that orchid mycorrhizal fungi may have a broad geographic distribution, but that their occurrence is bounded by specific habitat conditions.
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genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex
Heredity, 2016Co-Authors: Mikael Hedrén, Maria Tannhäuser, Maria Teresa Lorenzo, Francisco Balao, Ovidiu PaunAbstract: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.
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allotetraploid evolution in Dactylorhiza orchidaceae
Lankesteriana International Journal on Orchidology, 2015Co-Authors: Mark W. Chase, Mikael Hedrén, Richard M. Bateman, Michael F. Fay, Yohan PillonAbstract:One of the most perplexing problems in Western European terrestrial orchid taxonomy has been how to deal with the large numbers of taxa that have been described for the allopolyploid taxa, which are the products of hybridization between taxa in the Dactylorhiza maculata (L.) Soo group and the D. incarnata (L.) Soo group.
Richard M. Bateman - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae)
Systematic biology, 2019Co-Authors: Marie K. Brandrud, Mikael Hedrén, Mark W. Chase, Richard M. Bateman, Juliane Baar, Maria Teresa Lorenzo, Alexander Athanasiadis, Ovidiu PaunAbstract: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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Molecular and morphological phylogenetics of the digitate-tubered clade within subtribe Orchidinae s.s. (Orchidaceae: Orchideae)
Kew Bulletin, 2018Co-Authors: Richard M. Bateman, Alexander R. M. Murphy, Peter M. Hollingsworth, Michelle L. Hart, Ian Denholm, Paula J. RudallAbstract:The digitate-tubered clade ( Dactylorhiza s.l. plus Gymnadenia s.l.) within subtribe Orchidinae is an important element of the North-temperate orchid flora and has become a model system for studying the genetic and epigenetic consequences of organism-wide ploidy change. Here, we integrate morphological phylogenetics with Sanger sequencing of nrITS and the plastid region trnL-F in order to explore phylogenetic relationships and phenotypic character evolution within the clade. The resulting morphological phylogenies are strongly incongruent with the molecular phylogenies, instead reconstructing through parsimony the genus-level boundaries recognised by traditional 20th Century taxonomy. They raise fresh doubts concerning whether Pseudorchis is sister to Platanthera or to Dactylorhiza plus Gymnadenia . Constraining the morphological matrix to the topology derived from ITS sequences increased tree length by 20%, adding considerably to the already exceptional level of phenotypic homoplasy. Both molecular and morphological trees agree that D. viridis and D. iberica are the earliest-diverging species within Dactylorhiza (emphasising the redundancy of the former genus Coeloglossum ). Morphology and ITS both suggest that the former genus Nigritella is nested within (and thus part of) Gymnadenia , the Pyrenean endemic 'N.' gabasiana apparently forming a molecular bridge between the two radically contrasting core phenotypes. Comparatively short subtending molecular branches plus widespread (though sporadic) hybridisation indicate that Dactylorhiza and Gymnadenia approximate the minimum level of molecular divergence acceptable in sister genera. They share similar tuber morphologies and base chromosome numbers, and both genera are unusually prone to polyploid speciation. Another prominent feature of multiple speciation events within Gymnadenia is floral paedomorphosis. The 'traditional' morphological and candidate-gene approaches to phylogeny reconstruction are critically appraised.
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Clarified relationship between Dactylorhiza viridis and Dactylorhiza iberica renders obsolete the former genus Coeloglossum (Orchidaceae: Orchidinae)
Kew Bulletin, 2017Co-Authors: Richard M. Bateman, Paula J. RudallAbstract:Two decades have passed since DNA evidence first demonstrated an intimate relationship between the circumboreal species 'Coeloglossum' viride and the temperate Eurasian genus Dactylorhiza s.s. Most subsequent molecular phylogenies showed 'C.' viride to diverge after the D. incarnata group. The law of monophyly therefore dictated inclusion in Dactylorhiza of 'C.' viride, irrespective of its undeniably distinctive morphology. Those orchid enthusiasts still determinedly seeking reasons for retaining the genus Coeloglossum have often used as a justification the one published molecular study that suggested that D. viridis diverged earlier than D. incarnata. Interestingly, these respective phylogenetic positions are supported by recent data-rich studies based on next-generation sequencing. However, recent DNA phylogenies also show that D. iberica — long regarded as morphologically distinct but nonetheless universally accepted as belonging within the genus — diverged penecontemporaneously with D. viridis. Thus, in order to justify maintaining 'Coeloglossum' as a separate monotypic genus it would also be necessary to transfer D. iberica to a new monotypic genus, thus recognising two genera that are not only monotypic but also show only modest molecular divergence from the remaining dactylorchids. Examining in greater detail the morphology and micromorphology of D. viridis and D. iberica, we show that both species possess multiple morphological character states that are unique within the genus Dactylorhiza, but argue that greater phenotypic disparity is commonly the case in early-divergent lineages per se. Review of previous publications discussing D. iberica revealed little knowledge of its autecology, and contradictory DNA-based inferences that can be traced back to just two original specimens. We also suggest that morphological and molecular variation within both species has been under-estimated and under-explored.
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allotetraploid evolution in Dactylorhiza orchidaceae
Lankesteriana International Journal on Orchidology, 2015Co-Authors: Mark W. Chase, Mikael Hedrén, Richard M. Bateman, Michael F. Fay, Yohan PillonAbstract:One of the most perplexing problems in Western European terrestrial orchid taxonomy has been how to deal with the large numbers of taxa that have been described for the allopolyploid taxa, which are the products of hybridization between taxa in the Dactylorhiza maculata (L.) Soo group and the D. incarnata (L.) Soo group.
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Plastid and nuclear DNA marker data support the recognition of four tetraploid marsh orchids (Dactylorhiza majalis s.l., Orchidaceae) in Britain and Ireland, but require their recircumscription
Biological Journal of the Linnean Society, 2011Co-Authors: Mikael Hedrén, Sofie Nordström, Richard M. BatemanAbstract:Relationships among allotetraploid marsh orchids collectively assignable to Dactylorhiza majalis s.l. are exceptionally complex because of multiple origins, secondary hybridization with each other, and with their parental lineages, local adaptation, and genomic reorganization processes, all extending through time and space. We sampled 34 populations from Britain and Ireland in an attempt to simultaneously interpret patterns of genetic differentiation within and between populations. The material analysed consisted of 250 individuals that were examined for variation at five nuclear microsatellite loci, internal transcribed spacer (ITS), and plastid DNA. Once integrated, patterns of differentiation in the three molecular data sets show that the British and Irish members of the D. majalis s.l. complex should be assigned to a minimum of four genetically differentiated subgroups of equal status (either species or subspecies), broadly corresponding to the traditional D. majalis ssp. praetermissa, ssp. purpurella, ssp. occidentalis, and ssp. traunsteinerioides. UK plants previously attributed to 'Dactylorhiza lapponica' and given high conservation status have been shown to be genetically identical to ssp. traunsteinerioides. The endemic Hebridean marsh orchid, D. majalis ssp. ebudensis, genetically resembles ssp. traunsteinerioides. Dactylorhiza majalis 'ssp. cambrensis' could readily be accommodated within ssp. purpurella. Together, these observations reinforce a recent assertion that anthocyanin content has been over-weighted in previous morphologically based classifications of Dactylorhiza. Several study populations showed signs of hybridization and introgression with other allotetraploids, or their parental lineages, especially with D. incarnata s.l. However, ssp. praetermissa and ssp. traunsteinerioides were better separated than anticipated: southern populations widely regarded as mixed populations of the two taxa are arguably better treated as containing an unusually narrow-leaved, ecologically specialized form of ssp. praetermissa. Accepting this recircumscription means that the southern margins of the distributions of ssp. purpurella and ssp. traunsteinerioides now coincide, stretching from mid-Wales to the Humber Estuary of Yorkshire, and together indicating a significant genetic transition zone. Plastid haplotype data confirm that ssp. traunsteinerioides and ssp. praetermissa are relatively old polyploids derived from the Continental D. majalis s.l. complex, whereas ssp. purpurella and ssp. occidentalis may have more recent (most likely postglacial) origins within their current distributions. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 107-128. (Less)
Daniel Tyteca - One of the best experts on this subject based on the ideXlab platform.
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Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza
Scientific reports, 2016Co-Authors: Hans Jacquemyn, Daniel Tyteca, Mikael Hedrén, Michael Waud, Vincent S. F. T. Merckx, Rein Brys, Bart LievensAbstract:Orchid species are critically dependent on mycorrhizal fungi for completion of their life cycle, particularly during the early stages of their development when nutritional resources are scarce. As such, orchid mycorrhizal fungi play an important role in the population dynamics, abundance, and spatial distribution of orchid species. However, less is known about the ecology and distribution of orchid mycorrhizal fungi. In this study, we used 454 amplicon pyrosequencing to investigate ecological and geographic variation in mycorrhizal associations in fourteen species of the orchid genus Dactylorhiza. More specifically, we tested the hypothesis that variation in orchid mycorrhizal communities resulted primarily from differences in habitat conditions where the species were growing. The results showed that all investigated Dactylorhiza species associated with a large number of fungal OTUs, the majority belonging to the Tulasnellaceae, Ceratobasidiaceae and Sebacinales. Mycorrhizal specificity was low, but significant variation in mycorrhizal community composition was observed between species inhabiting different ecological habitats. Although several fungi had a broad geographic distribution, Species Indicator Analysis revealed some fungi that were characteristic for specific habitats. Overall, these results indicate that orchid mycorrhizal fungi may have a broad geographic distribution, but that their occurrence is bounded by specific habitat conditions.
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On the monophyly of Dactylorhiza Necker ex Nevski (Orchidaceae): is Coeloglossum viride (L.) Hartman a Dactylorhiza ?
Botanical Journal of the Linnean Society, 2006Co-Authors: Nicolas Devos, Olivier Raspé, Anne-laure Jacquemart, Daniel TytecaAbstract:Previous phylogenetic analyses of Orchidaceae subtribe Orchidinae resulted in the proposal to classify Coeloglossum viride (L.) Hartman within the genus Dactylorhiza in order to maintain its monophyly. In this paper, we report some results that contradict previous studies regarding the monophyly of the traditional Dactylorhiza and its phylogenetic relationship with Coeloglossum. Our results, which combine sequences of the internal and external transcribed spacers of the nuclear ribosomal DNA, support the monophyly of Dactylorhiza, with Coeloglossum being a sister clade. The position of C. viride in the phylogenetic tree, and the considerable morphological differences with respect to Dactylorhiza, incline us to retain both lineages as distinct genera.
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on the monophyly of Dactylorhiza necker ex nevski orchidaceae is coeloglossum viride l hartman a Dactylorhiza
Botanical Journal of the Linnean Society, 2006Co-Authors: Nicolas Devos, Olivier Raspé, Anne-laure Jacquemart, Daniel TytecaAbstract:Previous phylogenetic analyses of Orchidaceae subtribe Orchidinae resulted in the proposal to classify Coeloglossum viride (L.) Hartman within the genus Dactylorhiza in order to maintain its monophyly. In this paper, we report some results that contradict previous studies regarding the monophyly of the traditional Dactylorhiza and its phylogenetic relationship with Coeloglossum. Our results, which combine sequences of the internal and external transcribed spacers of the nuclear ribosomal DNA, support the monophyly of Dactylorhiza, with Coeloglossum being a sister clade. The position of C. viride in the phylogenetic tree, and the considerable morphological differences with respect to Dactylorhiza, incline us to retain both lineages as distinct genera.
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The evolution of Dactylorhiza (Orchidaceae) allotetraploid complex: insights from nrDNA sequences and cpDNA PCR-RFLP data.
Molecular phylogenetics and evolution, 2006Co-Authors: Nicolas Devos, Olivier Raspé, Daniel Tyteca, Anne-laure JacquemartAbstract:Sequence data from a portion of the external transcribed spacer (ETS) and from the internal transcribed spacers (ITS1 and ITS2) of 18S-26S nuclear ribosomal DNA were used together with chloroplast DNA PCR-RFLP data to unravel patterns of allotetraploid speciation within the Western European Dactylorhiza polyploid complex. A maximum likelihood tree based on combined ETS and ITS sequences suggests that the Western European Dactylorhiza allotetraploids have evolved by hybridization between four main diploid lineages. Cloned sequences and the topology of the ITS plus ETS tree indicate that the allotetraploid species D. elata, D. brennensis, and D. sphagnicola have originated from the autotetraploid D. maculata together with the diploid D. incarnata, while D. majalis, D. traunsteineri, and D. angustata seem to have evolved by hybridization between the D. fuchsii s.str and D. incarnata lineages. Finally, the diploid D. saccifera lineage seems to have been involved together with the D. incarnata lineage in the formation of the allotetraploid D. praetermissa. The observed congruence between the chloroplast tree and the ITS/ETS tree suggests a directional evolution of the nrDNA after polyploidization in favor of the maternal genome. Considered together with morphological, biogeographical, and ecological evidence, the molecular analysis leads us to recognize four species within the investigated allotetraploid complex, namely D. majalis, D. praetermissa, D. elata, and D. sphagnicola.
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Patterns of chloroplast diversity among western European Dactylorhiza species (Orchidaceae)
Plant Systematics and Evolution, 2003Co-Authors: N. Devos, Daniel Tyteca, O. Rasp�, R. A. Wesselingh, Anne-laure JacquemartAbstract:In Europe, the genus Dactylorhiza comprises a bewildering variety of forms that are difficult to sort into discrete species. Most Dactylorhiza species are diploid or tetraploid and contrasting hypotheses have been proposed to explain the complex variation within this group. Using PCR-RFLP analysis in eight putative species, we could identify four highly differentiated chloroplast DNA lineages. The first lineage (clade A) included the unique haplotype found in D. sambucina. Clade B grouped four haplotypes belonging mostly to D. incarnata. Clades C and D included 27 haplotypes detected in diploid D. fuchsii and in all tetraploid species investigated. Eighty percent of the chloroplast variation were consistent with currently accepted species boundaries. The imperfect agreement between chloroplast variation and species boundaries may be ascribed to incomplete lineage sorting and/or reticulation. Our cpDNA results provide strong evidence that the allotetrapolyploids have been formed through asymmetric hybridization with a member of the D. fuchsii / maculata group as the maternal parent
David Ståhlberg - One of the best experts on this subject based on the ideXlab platform.
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Systematics and conservation genetics of Dactylorhiza majalis ssp. elatior (Orchidaceae) on Gotland
Nordic Journal of Botany, 2012Co-Authors: Mikael Hedrén, Sofie Olofsson, Henrik Æ. Pedersen, David StåhlbergAbstract:A tall allotetraploid member of the Dactylorhiza incarnata/maculata complex with unspotted leaves and large pinkish flowers from the island of Gotland in the Baltic was examined for molecular variation patterns at five nuclear microsatellite loci, nuclear ITS and in plastid haplotypes. The allotetraploid was well separated from allopatric allotetraploids of similar appearance, including the western European D. majalis ssp. integrata (syn. D. praetermissa) and forms of D. majalis ssp. lapponica from mainland Sweden. It also differed from other allotetraploids distributed in the Baltic Sea region, including D. majalis ssp. baltica and D. majalis ssp. lapponica. It is here recognized as D. majalis ssp. elatior (Fr.) Hedren & H. A. Pedersen. Dactylorhiza osiliensis Pikner, described from Saaremaa (Estonia) is regarded as a synonym. The distribution covers Gotland, Saaremaa and possibly Hiiumaa. Dactylorhiza majalis ssp. elatior may have one or several recent origins within its present distribution area, and it contains no other molecular markers than those found in the parental D. incarnata var. incarnata and D. maculata ssp. fuchsii in the same area. It appears to have weak barriers towards secondary hybridization with its parental lineages. The situation is reminiscent to that of other young allotetraploids in the D. majalis s.l. complex, suggesting that introgression may be an underestimated process explaining the accumulation of genetic diversity in evolving allopolyploid plants.
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Geographical variation and systematics of the tetraploid marsh orchid Dactylorhiza majalis subsp sphagnicola (Orchidaceae) and closely related taxa
Botanical Journal of the Linnean Society, 2012Co-Authors: Mikael Hedrén, Sofie Olofsson, David StåhlbergAbstract:Dactylorhiza majalis subsp. sphagnicola is an allotetraploid marsh orchid derived from parents closely similar to present-day D. incarnata and the western European form of D. maculata subsp. maculata, suggesting that it has a postglacial origin. It extends from northwestern continental Europe into areas formerly covered by the Weichselian ice sheet in mid-Scandinavia. Here, we studied the variation at both the plastid and nuclear marker systems to describe the geographical variation in subsp. sphagnicola and its evolutionary history. We investigated whether subsp. sphagnicola is affected by secondary hybridization and gene flow from its parental lineages or from other allotetraploid marsh orchids, and we also compared subsp. sphagnicola with other allotetraploids of similar origins. We analysed 492 plants from 50 populations. Thirty-seven populations were collected as potential Dactylorhiza majalis subsp. sphagnicola, five as subsp. sesquipedalis (D. elata), one as D. elata subsp. brennensis, one as subsp. calcifugiens, one as subsp. occidentalis and the remaining five as populations with some affinity to subsp. lapponica (including D. traunsteineri). All populations were analysed for plastid haplotypes and nuclear internal transcribed spacer (ITS) allele frequencies, and a subset of 43 populations was analysed for five nuclear microsatellite loci. Dactylorhiza majalis subsp. sphagnicola was dominated by a single plastid haplotype that was also dominant in western European D. maculata subsp. maculata, and most of the alternative haplotypes differed by only one mutation from the dominant one. There was more variation in nuclear microsatellites and ITS, and the variation was geographically structured in these markers. Subspecies occidentalis and calcifugiens shared haplotypes with subsp. sphagnicola, whereas subsp. sesquipedalis and brennensis had other haplotypes. Dactylorhiza majalis subsp. sphagnicola may have a postglacial origin within its present continental distribution. It has incorporated genetic material from D. maculata subsp. maculata by secondary hybridization and introgression, and some northern populations have assimilated strongly divergent haplotypes from the northeastern form of D. maculata subsp. maculata. Subspecies sphagnicola has also evolved morphologically divergent local populations in the north that do not differ from the typical populations in genetic markers. It may form mixed populations with other allotetraploid subspecies of D. majalis and, at least at one site, it has become integrated with subsp. lapponica, demonstrating that independently derived allotetraploids may contribute to a common gene pool. Subspecies calcifugiens seems to be derived from subsp. sphagnicola, and further studies based on a larger sample may confirm that it is better recognized as a variety. The so-called D. elata subsp. brennensis is of hybrid origin and combines markers from subsp. sesquipedalis with markers from the D. majalis core complex, possibly subsp. majalis. The new combination Dactylorhiza majalis subsp. sesquipedalis (Willd.) H.A.Pedersen & Hedren comb. nov. is provided. (C) 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168, 174193. (Less)
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polyploid evolution and plastid dna variation in the Dactylorhiza incarnata maculata complex orchidaceae in scandinavia
Molecular Ecology, 2008Co-Authors: Mikael Hedrén, Sofie Nordström, David StåhlbergAbstract:The Dactylorhiza incarnata/maculata complex (Orchidaceae) was used as a model system to understand genetic differentiation processes in a naturally occurring polyploid complex with much of ongoing diversification and wide distribution in recently glaciated areas in northern Europe. Data were obtained for 12 hypervariable regions in the plastid DNA genome. A total of 166 haplotypes were found in a sample of 1099 plants. Allopolyploid taxa have inherited their plastid genomes from D. maculata s.l. Overall haplotype diversity of the combined group of allopolyploid taxa was comparable to that of maternal D. maculata s.l., but populations of allopolyploids were also more strongly differentiated from each other and contained lower numbers of haplotypes than populations of D. maculata s.l. In addition to haplotypes found in extant D. maculata s.l., the allopolyploids also contained several distinct and widespread haplotypes that were not found in any of the parental lineages. Some of these haplotypes were shared between widespread allopolyploids. Divergent allopolyploids with small distributions did not seem to originate from local polyploidization events, but rather as segregates of already existing allopolyploids. Genetic diversification of allopolyploid Dactylorhiza is the result of repeated polyploid formation, secondary hybridization and introgression between already existing polyploids and extant representatives of parental lineages, hybridization between independently derived polyploid lineages, and phyletic diversification in the group of allopolyploids. Although some polyploid taxa must have evolved after the last glaciation, genetic material from the parental lineages has been transferred continuously for longer periods of time. This combination of processes may explain the taxonomic complexity encountered in Dactylorhiza and other polyploid complexes distributed in previously glaciated parts of Europe.
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Polyploid evolution and plastid DNA variation in the Dactylorhiza incarnata/maculata complex (Orchidaceae) in Scandinavia.
Molecular ecology, 2008Co-Authors: Mikael Hedrén, Sofie Nordström, David StåhlbergAbstract:The Dactylorhiza incarnata/maculata complex (Orchidaceae) was used as a model system to understand genetic differentiation processes in a naturally occurring polyploid complex with much of ongoing diversification and wide distribution in recently glaciated areas in northern Europe. Data were obtained for 12 hypervariable regions in the plastid DNA genome. A total of 166 haplotypes were found in a sample of 1099 plants. Allopolyploid taxa have inherited their plastid genomes from D. maculata s.l. Overall haplotype diversity of the combined group of allopolyploid taxa was comparable to that of maternal D. maculata s.l., but populations of allopolyploids were also more strongly differentiated from each other and contained lower numbers of haplotypes than populations of D. maculata s.l. In addition to haplotypes found in extant D. maculata s.l., the allopolyploids also contained several distinct and widespread haplotypes that were not found in any of the parental lineages. Some of these haplotypes were shared between widespread allopolyploids. Divergent allopolyploids with small distributions did not seem to originate from local polyploidization events, but rather as segregates of already existing allopolyploids. Genetic diversification of allopolyploid Dactylorhiza is the result of repeated polyploid formation, secondary hybridization and introgression between already existing polyploids and extant representatives of parental lineages, hybridization between independently derived polyploid lineages, and phyletic diversification in the group of allopolyploids. Although some polyploid taxa must have evolved after the last glaciation, genetic material from the parental lineages has been transferred continuously for longer periods of time. This combination of processes may explain the taxonomic complexity encountered in Dactylorhiza and other polyploid complexes distributed in previously glaciated parts of Europe.
Mark W. Chase - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae)
Systematic biology, 2019Co-Authors: Marie K. Brandrud, Mikael Hedrén, Mark W. Chase, Richard M. Bateman, Juliane Baar, Maria Teresa Lorenzo, Alexander Athanasiadis, Ovidiu PaunAbstract: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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Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima
Molecular ecology, 2017Co-Authors: Francisco Balao, Juliane Baar, Maria Teresa Lorenzo, Emiliano Trucchi, Thomas M. Wolfe, Bao Hai Hao, Laura Sedman, Carolin Kosiol, Fabian Amman, Mark W. ChaseAbstract: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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allotetraploid evolution in Dactylorhiza orchidaceae
Lankesteriana International Journal on Orchidology, 2015Co-Authors: Mark W. Chase, Mikael Hedrén, Richard M. Bateman, Michael F. Fay, Yohan PillonAbstract:One of the most perplexing problems in Western European terrestrial orchid taxonomy has been how to deal with the large numbers of taxa that have been described for the allopolyploid taxa, which are the products of hybridization between taxa in the Dactylorhiza maculata (L.) Soo group and the D. incarnata (L.) Soo group.
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Chalcone synthase variation and phylogenetic relationships in Dactylorhiza (Orchidaceae)
Botanical Journal of the Linnean Society, 2010Co-Authors: Luis A. Inda, Manuel Pimentel, Mark W. ChaseAbstract:Different authors have demonstrated the usefulness of single-copy nuclear genes in unravelling the evolution of polyploid species' complexes. We used the chalcone synthase gene family to analyse relationships among several Dactylorhiza species belonging to the main diploid and tetraploid lineages of this genus and to evaluate relationships between Dactylorhiza and other orchid genera that traditionally have been considered to be closely related. Overall, 59 sequences from 19 taxa were analysed using parsimony and Bayesian inference. In our results, we recover a sister relationship between Dactylorhiza and Gymnadenia. In addition, our results support the idea that genera Coeloglossum and Dactylorhiza should be merged into one taxonomic entity. Finally, we add some information on the origin of allotetraploid Dactylorhiza taxa, such as D. praetermissa and D. elata. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163, 155–165.
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Evolution of Dactylorhiza baltica (Orchidaceae) in European Russia: evidence from molecular markers and morphology
Botanical Journal of the Linnean Society, 2005Co-Authors: Alexey Shipunov, Michael F. Fay, Mark W. ChaseAbstract:Four plastid markers, four nuclear markers and 14 morphometric characters were used in this study to investigate the evolution of Dactylorhiza baltica (Orchidaceae) in European Russia. In total, 98, 214 and 775 samples from 85, 112 and 121 populations were involved in the combined and separate molecular and morphometric analyses, respectively. In most cases, morphometric measures were done on exactly the same plants that were used for DNA studies. Dactylorhiza baltica plants from European Russia are most probably the products of several recent and mostly local hybridization events between the diploids D. fuchsii and D. incarnata, which have each been the maternal parent on different occasions. Considerable introgression into the parental diploids via the allopolyploid D. baltica is also hypothesized. Several morphological characters, such as length of the lip lateral lobe and the length of longest leaf, were found to be robust and could be useful in identification of D. baltica. This study demonstrates the advantage of ‘combined’ techniques, especially in the case of taxonomically complex taxa. © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society, 2005, 147, 257–274.
