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8 results for “low copy nuclear genes”
Data from: Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low-copy nuclear genes
DNA sequence data from the low-copy nuclear genes waxy (GBSSI) and leafy were compared with plastid sequence data from prior studies to reconstruct phylogenetic relationships in the Wintergreen Group of tribe Gaultherieae (Ericaceae). We conducted phylogenetic analysis with 109 species that includes representatives of all 15 major clades previously diagnosed in the Wintergreen Group and that together span its circum-Pacific distribution. Results yielded two distinct homeologous copies of waxy for two of the clades, each in widely separated parts of the tree. It also yielded two copies of leafy for one of the clades; only one copy of leafy was found for the other clade, but it was placed in the same major clade as its waxy counterpart and well away from its placement in a prior plastid analysis. A combined four-locus (waxy, leafy, ITS, and plastid loci) phylogenetic analysis of all available relevant data placed the copies of each of the clades in two distinct positions in the phylogeny with strong overall statistical support. In combination with evidence from morphology, reproductive biology, and cytology, the results suggest that these clades arose through allopolyploid hybridization between lineages deep in the phylogeny but relatively close geographically. This finding confirms previous assumptions that hybridization plays an important role in the evolution of the Gaultherieae.
Set of 4 597 baits designed in collaboration with RapidGenomics (Gainesville, Florida, USA) to capture the identified low‐ to single‐copy nuclear genes (LSCN).
<p>This dataset presents a set of 4,597 baits designed in collaboration with RapidGenomics (Gainesville, Florida, USA) to capture the identified low- to single-copy nuclear genes (LSCN) in our study. These baits were instrumental in our research on the evolutionary relationships of the Neotropical magnolias based on plastome and nuclear phylogenomics. The data provided are crucial for understanding the methodology and results of our study.</p>
Data from: Low-copy nuclear genes reveal new evidence of incongruence in relationships within Malvaceae s.l.
<p>The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s.l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plant Project (1KP) and publicly available genome information from cotton, cacao, and <i>Arabidopsis, </i>we designed a set of molecular markers of potentially single-or low-copy nuclear genes for Malvaceae s.l. Phylogenetic potential of these new loci was compared to previously applied conventional markers (i.e., plastid <i>trnK</i>-<i>matK</i> region and <i>rbcL</i> gene and the <a>nrDNA </a>ITS region) using the phylogenetic informativeness method. The results show that, when the mined nuclear regions are used in combination, it is possible to resolve relationships at different taxonomic levels within the phylogeny. However, incongruence among nuclear loci is frequent in the group, explaining the prevalence of unresolved phylogenetic relationships.</p>
Data from: Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low-copy nuclear genes
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Data from: Low-copy nuclear genes reveal new evidence of incongruence in relationships within Malvaceae s.l.
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Data from: Phylogenetic relationships in Orobanchaceae inferred from low-copy nuclear genes: consolidation of major clades and identification of a novel position of the non-photosynthetic Orobanche clade sister to all other parasitic Orobanchaceae
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Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes
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 35877 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 ∼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.
Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes
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