Find research datasets worth reusing

opencc-by-4.0Oct 2020View details →

Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Data used in phylogenomic analyses of manakin birds.  Datasets number 1 to 7 include sequence alignments for each locus analyzed, and datasets 4 to 7 also contain gene trees used as input for ASTRAL.

opencc-by-4.0Dec 2020View details →

Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperm-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group.

opencc-by-4.0Mar 2017View details →

A phylogenomics resource for the marine diatom Pseudo-nitzschia multistriata

The resource contains phylogenetic trees built from approximately 9000 P. multistriata genes, comparing them to their orthologs (over 2 million sequences) across major taxa of archaea, bacteria and eukaryotes (Basu et al., 2017). For each orthologous group a tree is built twice using two different substitution models. Each sequence within a tree is given a specific ID which is a combination of a unique number along with a taxonomy code, for example "alla_stramenopile|34" signifies 1) alla: organism Albugo laibachii. 2) stramenopile: broad taxonomic class. 3) 34: protein ID for Albugo laibachii DNA topoisomerase 2. The mapping between Pseudo-nitzschia multistriata proteins and the phylogenetic trees is present in the file "p.multistriata_gene_tree.txt". The detailed description of each protein ID given in any phylogenetic tree is present in the file "geneDB.txt". The phylogenetic trees generated using JTT and WAG substitution models of the FastTree program as present in the folders "treeJTT", "treeWAG".

opencc-by-4.0Nov 2024View details →

MATEdb2, a Collection of High-Quality Metazoan Proteomes across the Animal Tree of Life to Speed Up Phylogenomic Studies

Recent advances in high-throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to the high cost of genome sequencing, the high complexity of assembly, and the lack of standardized protocols for genome annotation. The lack of consensus in the annotation and publication of genome files hinders research by making researchers lose time in reformatting the files for their purposes but can also reduce the quality of the genetic repertoire for an evolutionary study. Thus, the use of transcriptomes obtained using the same pipeline as a proxy for the genetic content of species remains a valuable resource that is easier to obtain, cheaper, and more comparable than genomes. In a previous study, we presented the Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla, Arthropoda and Mollusca. Here, we present the newest version of MATEdb (MATEdb2) that overcomes some of the previous limitations of our database: (i) we include data from all animal phyla where public data are available, and (ii) we provide gene annotations extracted from the original GFF genome files using the same pipeline. In total, we provide proteomes inferred from high-quality transcriptomic or genomic data for almost 1,000 animal species, including the longest isoforms, all isoforms, and functional annotation based on sequence homology and protein language models, as well as the embedding representations of the sequences. We believe this new version of MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open, greener, and collaborative science.

opencc-by-4.0Jun 2022View details →

Research data for UCE phylogenomics of sawflies and woodwasps

Input files, scripts and newick tree files for the ongoing project on reconstructing a comprehensive phylogeny and biogeography for sawflies and woodwasps (Hymenoptera).

opencc-by-4.0Jul 2022View details →

Alignment used in "A phylogenomically informed five-order system for the closest relatives of land plants"

Alignment that served as the basis for the phylogenomic analyses presented in "A phylogenomically informed five-order system for the closest relatives of land plants" — preprint on bioRxiv doi: https://doi.org/10.1101/2022.07.06.499032

opencc-by-4.0Oct 2022View details →

Data set: Australia's hidden radiation - phylogenomic analysis reveals rapid Miocene radiation of blindsnakes

This repository contains the additional raw data to accompany our paper entitled "Australia’s hidden radiation: phylogenomic analysis reveals rapid Miocene radiation of blind snakes." This project is part of the AusARG Initiative funded by BioPlatforms Australia. Raw sequences data can be downloaded from the BioPlatforms downloads portal: https://data.bioplatforms.com/dataset?q=ticket%3ABPAOPS-1196 Information about files <ol> <li>ASTRAL_tree_SqCL_AHE.tre - output from ASTRAL-III just with SqCL data + outgroups</li> <li>ASTRAL_tree_SqCL_AHE_Ramphotyphlops.tre - same with above but also  including additional Ramphotyphlops genes.</li> <li>mcmctree_1.txt - mcmcfile output from MCMCTree analysis using all SkewT or SkewNormal distribution priors.</li> <li>mcmctree_2.txt - mcmcfile output from MCMCTree analysis using SkewT, SkewNormal, and cauchy distribution priors. **This is the tree used in our publication**</li> <li>mcmctree_strategy1.tre - output phylogeny 1</li> <li>mcmctree_strategy2.tre - output phylogeny 2</li> <li>IQTREE_gcf_scf.nex - gene concordance and site factors for mcmctree_strategy2.tre</li> </ol> tree_data/ folder contains concatenated gene trees (IQTREE) and corresponding shortcut coalescent method (ASTRAL-III) tree. Should there be questions regarding the code and data set, please contact the corresponding author.

opencc-by-4.0Jun 2024View details →

Datasets for the Phylogenomic Study of the Fleshy-Fruited Sonerileae (Melastomataceae)

This repository contains datasets used in the phylogenomic analysis of the fleshy-fruited Sonerileae (Melastomataceae). The data include various gene alignments, gene trees, and species trees.

opencc-by-4.0Oct 2019View details →

Data from: Paule et al. (2020) Phylogenomic insights into the Fascicularia-Ochagavia group (Bromelioideae, Bromeliaceae). Botanical Journal of the Linnean Society (doi: 10.1093/botlinnean/boz085)

DNA sequence alignments as well as the input and output files which specify the different data partitioning schemes used for phylogenetic analyses in Paule et al. (2020) Phylogenomic insights into the Fascicularia-Ochagavia group (Bromelioideae, Bromeliaceae). Botanical Journal of the Linnean Society (doi: 10.1093/botlinnean/boz085).

Fig. 12 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 12. Distribution map, face view, and lateral view of petiole of Rasopone JTL030 (worker, Panama, CASENT0633075), R. JTL037 (worker, Guatemala, CASENT0625283), R. mesoamericana (holotype worker), and R. JTL029 (worker, Panama, CASENT0633053). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 13 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 13. Distribution map, face view, and lateral view of petiole of Rasopone cubitalis (holotype worker), R. titanis (worker, Mexico, Chiapas, MCZ-ENT00716640), R. breviscapa (holotype queen), and R. rupinicola (worker, Colombia, face view MCZ-ENT00716589, petiole CASENT0217567). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 11 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 11. Distribution map, face view, and lateral view of petiole of Rasopone ferruginea (worker, Nicaragua, CASENT0644264), R. JTL040 (worker, Colombia, MCZ-ENT00716609), R. JTL041 (worker, Colombia, MCZ-ENT00716614), and R. costaricensis form a (worker, Costa Rica, INB0003659312). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality (type locality for R. ferruginea is 'Mexico').

Fig. 8 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 8. Distribution map, face view, and lateral view of petiole of Rasopone lunaris (worker, Brazil, Minas Gerais CASENT0644556), R. guatemalensis (holotype worker), R. costaricensis form c (worker, Costa Rica, INB0003659307), and R. JTL027 (worker, Panama, CASENT0633216). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 7 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 7. Distribution map, face view, and lateral view of petiole of Rasopone MAS010 (worker, Costa Rica, 08COSTA-1723), R. cryptergates (worker, Costa Rica, INB0003660648), R. JTL042 (worker, Colombia, MCZ-ENT00716611), and R. JTL034 (worker, Mexico, CASENT0640282). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 2 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 2. Phylogeny of Rasopone, Mayaponera, and selected outgroup taxa, inferred using the program IQ-TREE and 1,802 UCE loci. Node support values (ultrafast bootstrap/SH-like) <100/100 are depicted with red dots. Terminal names show original, morphology-based species assignments and depict morphological convergence across clades. The 'EX#' code in terminal names indicate unique extraction codes that link specimens to specimen data in provided tables. Simopelta andersoni, a distant outgroup, is not shown in the figure. Images depict workers of Rasopone ferruginea (Nicaragua, CASENT0644264), Mayponera becculata (Peru, CASENT0374638, modified from AntWeb, credit Michele Esposito), and Mayaponera constricta (Bolivia, CASENT0249137, modified from AntWeb, credit Ryan Perry).

Fig. 1 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 1. Characteristics of Rasopone species. (A) Habitus. (B) Scale-like petiole, showing definitions of petiole height (PTH) and petiole length (PTL), and the distinctive shape of the sternite. (C) Petiolar node intermediate between scale-like and cuboidal. (D) Cuboidal petiolar node. (E) Anterior clypeal margin truncate, with angulate lateral lobes. (F) Anterior clypeal margin sinuous, with rounded lateral lobes.

Fig. 6 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 6. Distribution map, face view, and lateral view of petiole of Rasopone pluviselva (holotype worker), R. minuta (worker, Mexico, Chiapas, CASENT0609834), R. JTL043 (worker, Ecuador, MCZ-ENT00716620), and R. JTL048 (worker, French Guiana, CASENT0645961). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 4 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 4. Dealate queen of Rasopone ferruginea (Nicaragua, CASENT0624181). Scale bars are 0.5 mm for face view, 1.0 mm for dorsal and lateral views.