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Abstract We reconstruct the species-level phylogenetic relationship among toucans, toucan-barbets, New World barbets using phylogenomic data to assess the monophyly and relationships at the family, generic, and specific levels. Our analyses confirmed (1) the monophyly of toucans (Aves: Ramphastidae), toucan-barbets (Aves: Semnornithidae), and New World barbets (Aves: Capitonidae) and that the toucan-barbets are sister to the toucans, an arrangement suggested, but poorly supported, in previously published phylogenies; (2) the paraphyly of lowland Selenidera toucanets with respect to Andigena mountain-toucans; and (3) evidence of some mitonuclear discordance, suggesting introgression or incomplete lineage sorting. For example, mitonuclear conflict in the phylogenetic placement of Ramphastos vitellinus subspecies suggests that Amazonian populations of Ramphastos vitellinus ariel may have introgressed mitogenomes derived from other Amazonian vitellinus taxa. To reconstruct the phylogenetic history of toucans, toucan-barbets, and New World barbets, we included all species-level taxa from the three families, with the addition of outgroups from the two major clades of Old World barbets (Megalaimidae and Lybiidae). We analyzed a combination of UCE sequences and whole mitochondrial genome sequences to reconstruct phylogenetic trees.
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In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
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- Award ID(s):
- 2027458
- PAR ID:
- 10340108
- Date Published:
- Journal Name:
- Frontiers in Fungal Biology
- Volume:
- 2
- ISSN:
- 2673-6128
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/ffunb.2021.716385
