Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales
| Main Authors: | Walker, Joseph Frederic, Yang, Ya, Feng, Tao, Timoneda, Alfonso, Mikenas, Jessica, Hutchison, Vera, Edwards, Caroline, Wang, Ning, Ahluwalia, Sonia, Olivieri, Julia, Walker-Hale, Nathanael, Majure, Lucas C., Puente, Raúl, Kadereit, Gudrun, Lauterbach, Maximillian, Eggli, Urs, Flores-Olvera, Hilda, Ochoterena, Helga, Brockington, Samuel F., Moore, Michael J., Smith, Stephen A. |
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| Format: | info dataset Journal |
| Terbitan: |
, 2019
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4948989 |
Daftar Isi:
- Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene tree conflict analyses. Key Results— Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is a common feature of phylogenomic studies but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. Conclusions— Transcriptomes are useful both for species tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large datasets.
- Dryad.tgzYou can untar and unzip with tar -xzvf Dryad.tgz. This will create one folder called Dryad. In that folder there are four separate folders. The first contains the 305 species tree and orthologs used to create the tree, seen in figure 3 of the publication. The Next is the Assemblies, these are in both PEP and CDS, they are associated with their keys but those can be changed using the NameKey.txt file. The next folder is FamilyAnalyses, this contains the orthologs, conflict analysis and species tree analyses for the five major families analyzed. The final folder is programs which contains a set of scripts used for the analysis.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB 1054539, DEB 1352907 and DEB 1354048