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- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 5. |
- Li, Fay-Wei, et al.
(författare)
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Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
- 2014
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:18, s. 6672-6677
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Tidskriftsartikel (refereegranskat)abstract
- Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
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| 6. |
- Rothfels, Carl J., et al.
(författare)
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The evolutionary history of ferns inferred from 25 low-copy nuclear genes
- 2015
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Ingår i: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 102:7, s. 1089-1107
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Tidskriftsartikel (refereegranskat)abstract
- PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35 877 bp), along with rigorous alignment, orthology inference and model selection. KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to similar to 200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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| 7. |
- Rothfels, Carl J., et al.
(författare)
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Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:10, s. e76957-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. Principal Findings: We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. Conclusions: The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.
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- Bürge, Teresa, 1986, et al.
(författare)
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Ivory at the Transition from the Late Bronze to the Early Iron Age in Transjordan: Trade and Distribution
- 2018
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Ingår i: Proceedings of the 10 th International Congress on the Archaeology of the Ancient Near East, 25–29 April 2016, Vienna / Edited by Barbara Horejs, Christoph Schwall, Vera Müller, Marta Luciani, Markus Ritter, Mattia Guidetti, Roderick B. Salisbury, Felix Höflmayer and Teresa Bürge. Volume 2.. - Wiesbaden : Harrassowitz.
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Konferensbidrag (refereegranskat)abstract
- Ivory is regarded as one of the most important exotic luxury items in the Eastern Mediterranean and the Near East. The aim of this paper is to provide an overview of ivory objects from Transjordan in the Middle Bronze Age and, specifically, the Late Bronze Age and the transition to the Iron Age. Their styles and foreign influences will be discussed. These objects prove the continuing demand for ivory in this region and show that Transjordan, which belonged to the Eastern Mediterranean cultural sphere, was part of the “international” trade network.
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| 9. |
- Bürge, Teresa, 1986, et al.
(författare)
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Nuragic pottery from Hala Sultan Tekke: The Cypriot-Sardinian connection
- 2019
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Ingår i: Egypt and the Levant. - 1015-5104 .- 1813-5145. ; 29, s. 231-244
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Tidskriftsartikel (refereegranskat)abstract
- The present paper describes, for the first time, Cypriot evidence of Nuragic tableware from Sardinia discovered at Hala Sultan Tekke. This Late Bronze Age harbour and trade metropolis is situated near modern Larnaca on the southern littoral of Cyprus. The city's exceptional wealth during the Late Bronze Age (1650-1050 BCE) was based on trade and cross-cultural connections with a vast area, including the entire Aegean, Anatolia, the Levant and Egypt. This is exemplified by the enormous amount of imported goods, most of which originated in the Mycenaean sphere of culture. Five handmade and burnished bowls of dark grey fabric with highly lustrous surfaces found at Hala Sultan Tekke were recently identified as imports from Sardinia. The main purpose of this article is to provide primary information about these exceptional finds and to place them in the context of trade between Sardinia and the eastern Mediterranean.
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