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  • 1
    In: PLoS ONE, Public Library of Science (PLoS), Vol. 7, No. 8 ( 2012-8-3), p. e42691-
    Type of Medium: Online Resource
    ISSN: 1932-6203
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2012
    detail.hit.zdb_id: 2267670-3
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  • 2
    In: Molecular Phylogenetics and Evolution, Elsevier BV, Vol. 128 ( 2018-11), p. 55-68
    Type of Medium: Online Resource
    ISSN: 1055-7903
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2018
    detail.hit.zdb_id: 1471402-4
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Botanical Journal of the Linnean Society Vol. 192, No. 4 ( 2020-03-27), p. 642-655
    In: Botanical Journal of the Linnean Society, Oxford University Press (OUP), Vol. 192, No. 4 ( 2020-03-27), p. 642-655
    Abstract: Ochagavia (four species) and Fascicularia (one species) form a well-supported clade of the early-diverging Bromelioideae. The two genera are morphologically similar, but they can be easily discerned on the basis of generative characters. Besides the species distributed on the Chilean mainland, the group includes O. elegans, endemic to the Robinson Crusoe Island of the Juan Fernández Islands. In previous molecular phylogenetic studies, O. elegans formed a sister clade to the remainder of Fascicularia and Ochagavia. A phylogenomic approach, including nearly complete and, in five cases, full plastomes (c. 160 kbp) and the nuclear rDNA cistron (c. 6 kbp), and scanning electron microscope (SEM) images of pollen were used to analyse relationships in the Fascicularia-Ochagavia group. Plastome and nuclear trees were largely congruent and supported previous phylogenetic analyses of O. elegans being sister to the remainder of the group. A divergent phylogenetic position was suggested for O. carnea using different organellar trees. SEM analysis of pollen supported the division of Fascicularia and Ochagavia. Evolutionary and taxonomic implications of our results are discussed.
    Type of Medium: Online Resource
    ISSN: 0024-4074 , 1095-8339
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1462255-5
    SSG: 12
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  • 4
    In: Annals of Botany, Oxford University Press (OUP), Vol. 131, No. 1 ( 2023-02-07), p. 71-86
    Abstract: Reproductive isolation and local establishment are necessary for plant speciation. Polyploidy, the possession of more than two complete chromosome sets, creates a strong postzygotic reproductive barrier between diploid and tetraploid cytotypes. However, this barrier weakens between polyploids (e.g. tetraploids and hexaploids). Reproductive isolation may be enhanced by cytotype morphological and environmental differentiation. Moreover, morphological adaptations to local conditions contribute to plant establishment. However, the relative contributions of ploidy level and the environment to morphology have generally been neglected. Thus, the extent of morphological variation driven by ploidy level and the environment was modelled for diploid, tetraploid and hexaploid cytotypes of Campanula rotundifolia agg. Cytotype distribution was updated, and morphological and environmental differentiation was tested in the presence and absence of natural contact zones. Methods Cytotype distribution was assessed from 231 localities in Central Europe, including 48 localities with known chromosome counts, using flow cytometry. Differentiation in environmental niche and morphology was tested for cytotype pairs using discriminant analyses. A structural equation model was used to explore the synergies between cytotype, environment and morphology. Key Results Tremendous discrepancies were revealed between the reported and detected cytotype distribution. Neither mixed-ploidy populations nor interploidy hybrids were detected in the contact zones. Diploids had the broadest environmental niche, while hexaploids had the smallest and specialized niche. Hexaploids and spatially isolated cytotype pairs differed morphologically, including allopatric tetraploids. While leaf and shoot morphology were influenced by environmental conditions and polyploidy, flower morphology depended exclusively on the cytotype. Conclusions Reproductive isolation mechanisms vary between cytotypes. While diploids and polyploids are isolated postzygotically, the environmental niche shift is essential between higher polyploids. The impact of polyploidy and the environment on plant morphology implies the adaptive potential of polyploids, while the exclusive relationship between flower morphology and cytotype highlights the role of polyploidy in reproductive isolation.
    Type of Medium: Online Resource
    ISSN: 0305-7364 , 1095-8290
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1461328-1
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  • 5
    In: Applications in Plant Sciences, Wiley, Vol. 2, No. 9 ( 2014-09)
    Abstract: • Premise of the study: Hyb‐Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low‐copy nuclear genes and high‐copy genomic targets for plant systematics and evolution studies. • Methods and Results: Genome and transcriptome assemblies for milkweed ( Asclepias syriaca ) were used to design enrichment probes for 3385 exons from 768 genes ( 〉 1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb‐Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length 〉 2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off‐target reads. Phylogenomic analyses demonstrated signal conflict between genomes. • Conclusions: The Hyb‐Seq approach enables targeted sequencing of thousands of low‐copy nuclear exons and flanking regions, as well as genome skimming of high‐copy repeats and organellar genomes, to efficiently produce genome‐scale data sets for phylogenomics.
    Type of Medium: Online Resource
    ISSN: 2168-0450 , 2168-0450
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2699923-7
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  • 6
    In: Applications in Plant Sciences, Wiley, Vol. 7, No. 10 ( 2019-10)
    Abstract: Hybrid capture with high‐throughput sequencing (Hyb‐Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family‐specific Hyb‐Seq probe set and the outcomes of different phylogenetic analyses are investigated here. Methods Hyb‐Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non‐paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. Results Alignments of the Asteraceae family‐wide Hyb‐Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. Discussion The approach used to build a Hyb‐Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb‐Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage‐specific.
    Type of Medium: Online Resource
    ISSN: 2168-0450 , 2168-0450
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2699923-7
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  • 7
    In: Molecular Ecology Resources, Wiley, Vol. 16, No. 5 ( 2016-09), p. 1124-1135
    Abstract: Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear ( LCN ) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region. This resulted in 1164 LCN genes greater than 600 bp. Using target enrichment combined with genome skimming (Hyb‐Seq), we obtained on average 1141 LCN loci, nearly the whole plastid genome and the nr DNA cistron from 23 southern African Oxalis species. Despite a wide range of gene trees, the phylogeny based on the LCN genes was very robust, as retrieved through various gene and species tree reconstruction methods as well as concatenation. Cytonuclear discordance was strong. This indicates that organellar phylogenies alone are unlikely to represent the species tree and stresses the utility of Hyb‐Seq in phylogenetics.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2406833-0
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  • 8
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2011
    In:  Proceedings of the National Academy of Sciences Vol. 108, No. 34 ( 2011-08-23), p. 14192-14197
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 108, No. 34 ( 2011-08-23), p. 14192-14197
    Abstract: The genus Arabidopsis provides a unique opportunity to study fundamental biological questions in plant sciences using the diploid model species Arabidopsis thaliana and Arabidopsis lyrata . However, only a few studies have focused on introgression and hybrid speciation in Arabidopsis , although polyploidy is a common phenomenon within this genus. More recently, there is growing evidence of significant gene flow between the various Arabidopsis species. So far, we know Arabidopsis suecica and Arabidopsis kamchatica as fully stabilized allopolyploid species. Both species evolved during Pleistocene glaciation and deglaciation cycles in Fennoscandinavia and the amphi-Beringian region, respectively. These hybrid studies were conducted either on a phylogeographic scale or reconstructed experimentally in the laboratory. In our study we focus at a regional and population level. Our research area is located in the foothills of the eastern Austrian Alps, where two Arabidopsis species, Arabidopsis arenosa and A. lyrata ssp. petraea , are sympatrically distributed. Our hypothesis of genetic introgression, migration, and adaptation to the changing environment during the Pleistocene has been confirmed: We observed significant, mainly unidirectional gene flow between the two species, which has given rise to the tetraploid A. lyrata . This cytotype was able to escape from the narrow ecological niche occupied by diploid A. lyrata ssp. petraea on limestone outcrops by migrating northward into siliceous areas, leaving behind a trail of genetic differentiation.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2011
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
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  • 9
    In: BMC Evolutionary Biology, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2010-12)
    Abstract: The genomes of higher plants are, on the majority, polyploid, and hybridisation is more frequent in plants than in animals. Both polyploidisation and hybridisation contribute to increased variability within species, and may transfer adaptations between species in a changing environment. Studying these aspects of evolution within a diversified species complex could help to clarify overall spatial and temporal patterns of plant speciation. The Arabidopsis lyrata complex, which is closely related to the model plant Arabidopsis thaliana , is a perennial, outcrossing, herbaceous species complex with a circumpolar distribution in the Northern Hemisphere as well as a disjunct Central European distribution in relictual habitats. This species complex comprises three species and four subspecies, mainly diploids but also several tetraploids, including one natural hybrid. The complex is ecologically, but not fully geographically, separated from members of the closely related species complex of Arabidopsis halleri , and the evolutionary histories of both species compexes have largely been influenced by Pleistocene climate oscillations. Results Using DNA sequence data from the nuclear encoded cytosolic phosphoglucoisomerase and Internal Transcribed Spacers 1 and 2 of the ribosomal DNA, as well as the trn L/F region from the chloroplast genome, we unravelled the phylogeography of the various taxonomic units of the A. lyrata complex. We demonstrate the existence of two major gene pools in Central Europe and Northern America. These two major gene pools are constructed from different taxonomic units. We also confirmed that A. kamchatica is the allotetraploid hybrid between A. lyrata and A. halleri , occupying the amphi-Beringian area in Eastern Asia and Northern America. This species closes the large distribution gap of the various other A. lyrata segregates. Furthermore, we revealed a threefold independent allopolyploid origin of this hybrid species in Japan, China, and Kamchatka. Conclusions Unglaciated parts of the Eastern Austrian Alps and arctic Eurasia, including Beringia, served as major glacial refugia of the Eurasian A. lyrata lineage, whereas A. halleri and its various subspecies probably survived in refuges in Central Europe and Eastern Asia with a large distribution gap in between. The North American A. lyrata lineage probably survived the glaciation in the southeast of North America. The dramatic climatic changes during glaciation and deglaciation cycles promoted not only secondary contact and formation of the allopolyploid hybrid A. kamchatica , but also provided the environment that allowed this species to fill a large geographic gap separating the two genetically different A. lyrata lineages from Eurasia and North America. With our example focusing on the evolutionary history of the A. lyrata species complex, we add substantial information to a broad evolutionary framework for future investigations within this emerging model system in molecular and evolutionary biology.
    Type of Medium: Online Resource
    ISSN: 1471-2148
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2010
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    detail.hit.zdb_id: 3053924-9
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  • 10
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2014
    In:  BMC Evolutionary Biology Vol. 14, No. 1 ( 2014-12)
    In: BMC Evolutionary Biology, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2014-12)
    Type of Medium: Online Resource
    ISSN: 1471-2148
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2014
    detail.hit.zdb_id: 2041493-6
    detail.hit.zdb_id: 3053924-9
    SSG: 12
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