Find research datasets worth reusing

opencc-by-4.0May 2019View details →

FIGURE 1 in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 1. Strict consensus cladogram of nine most parsimonious trees (length: 2038, CI: 0.2498, RI: 0.5337, RC: 0.1333, HI: 0.7502) from analysis of our new morphological dataset of 40 taxa and 368 characters in PAUP*. Results support optimization of an Aptornis defossor + Psophia obscura sister group. Synapomorphies are detailed in table 2. Extinct taxa are denoted with daggers. Bootstrap support values greater than 50% are annotated above branches, with branch length ranges reported below branches.

opencc-by-4.0May 2019View details →

FIGURE 3. A in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 3. A. Resulting tree from Bayesian analysis of 32 RAG1 and RAG2 sequences. Clade credibility values greater than 90% are annotated above branches. Core Gruiformes, Ralloidea, and Gruoidea are well supported with 100% clade credibility values. The scale bar at the bottom of the tree denotes branch length. The data were run in MrBayes for 2,000,000 generations.

opencc-by-4.0May 2019View details →

FIGURE 3 in A new morphological dataset reveals a novel relationship for the adzebills of New Zealand (Aptornis) and provides a foundation for total evidence neoavian phylogenetics

FIGURE 3 (continued). B. Resulting tree from Bayesian analysis of our new dataset of 40 taxa and 368 osteological characters combined with 32 sequences of RAG1 and RAG2 nuclear genes. Clade credibility values greater than 90% are annotated above branches. Extinct taxa are denoted with daggers. The scale bar at the bottom of the tree denotes branch length. The data were run in MrBayes for 1,100,000 generations.

opencc-by-4.0Nov 2022View details →

Dataset and R Code for Species-level Avian Influenza Phylogenetic Generalized Least Squares Regression

Dataset for Species-level Avian Influenza Phylogenetic Generalized Least Squares (PGLS) Regression: Variables include taxonomic information for each species, # of IAV-positive individuals, # of IAV-tested individuals, the prevalence of IAV, the proportion of diet made up of different food types, the proportion of foraging time spent in different strata (below water, water surface, ground, understory, etc), sampling-related variables (mean latitude, mean date, the proportion of hatch year individuals), migration and territoriality category, climatologic variables, mean clutch size, and mating system. R Code for PGLS and Avian Influenza Prevalence ContMap.

opencc-by-4.0Dec 2022View details →

Phylogenetic profile of 100 annotated low complexity proteins against the Uniprot Reference Proteome dataset

Phylogenetic profile of 100 human proteins with characteristic compositional bias, previously recorded by Mier et al (2020) against the Uniprot Reference Proteome, containing a total of 11297 proteomes, excluding viruses. The counts for each protein correspond to homologs found in each proteome.  Detailed description of included columns: ref_proteome_identifier: The Uniprot Reference Proteome identifier ncbi_taxid: The NCBI taxonomy ID species_name: NCBI common name corresponding to taxonomy ID species_code: internal species code composed of 9 characters taxonomic domain: E/B/A for Eukaryota/Bacteria/Archaea classification of proteome

dryad40/100

The Dayhoff Exchange Score: A new metric to quantify site saturation in amino acid datasets prior to phylogenetic analysis

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publicDec 2025View details →

dryad40/100

Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs

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publicOct 2021View details →

opencc-by-4.0Aug 2019View details →

Dataset for: "Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses"

This is the dataset and results folders for the manuscript titled "Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses". The dataset is necessary to run the code that can be found at <a href="https://github.com/adamhockenberry/dca-weighting">https://github.com/adamhockenberry/dca-weighting</a>

opencc-by-4.0Nov 2020View details →

Phylogenetic analysis of Harmonin Homology Domains - Datasets

Datasets associated to the article Phylogenetic analysis of Harmonin Homology Domains. HHD_starting-profile.hmm -> Profile HMM used to screen the UniprotKB HHD_all-hits_aligned.fa -> All hits aligned Other *.fa correspond to sequences identified for each cluster described in th article

opencc-zeroFeb 2020View details →

Implementing large genomic SNP datasets in phylogenetic network reconstructions: a case study of particularly rapid radiations of cichlid fish

The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua, are an extraordinary adaptive rapid radiation (<24,000 years old; 13 described species). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of ILS, as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just incomplete lineage sorting, but also gene flow, under the multispecies network coalescent model (MSNC), processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic dataset to date (RADseq dataset of 679 individuals and >37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation.

opencc-zeroNov 2023View details →

Phylogenetic dataset of clade Benthamidia of Cornus for biogeographic analysis of big-bracted dogwoods

The big-bracted dogwood clade Benthamidia of Cornus is a typical example of the well-known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than in NA. The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective. We generated RAD-seq data, conducted phylogenomic and biogeographic analyses for the clade with sampling of all species (9) and subspecies (10) currently recognized in floras.

opencc-by-4.0Dec 2023View details →

Datasets of the paper: Phylogenetic Insights into Central European Chorthippus and Pseudochorthippus (Orthoptera: Acrididae) Species Using ddRADseq Data

Alignments, trees & tree files, Structure plots & structure input files, and a table with relevant metadata of the paper "Phylogenetic Insights into Central European Chorthippus and Pseudochorthippus (Orthoptera: Acrididae) Species Using ddRADseq Data"

opencc-by-4.0Apr 2024View details →

Phylogenetic trees and morphological traits dataset of Geonoma palm genus

The phylogenetic trees correspond to the Geonoma genus and Geonomateae tribe phylogenies based on a concatenation analysis of 20 small informative genes and the csv file corresponds to the mean value of 24 morphological traits for 68 Geonoma species based on Henderson (2012) dataset.

opencc-zeroJul 2022View details →

Getting to know our biomonitor neighbours: urban lichens and allied fungi of Edmonton, Alberta, Canada: Phylogenetic Datasets

Here we provide one of the first detailed studies of lichen and allied fungi diversity in a continental North American city (Edmonton, Alberta, Canada), including an annotated checklist, images of all species, dichotomous keys, and local distribution maps. Edmonton is the northernmost city in North America with a population of over one million, and an industrial and transportation gateway for much of northern Canada. Lichen-based biomonitoring could be a tool to track airborne pollutants resulting from Edmonton's growing populace and industrial activity. The first step towards such a program is documenting the diversity and distribution of lichens in the city. To accomplish this, we conducted a city-wide, systematic survey of 191 sites focused on epiphytes growing on deciduous boulevard trees. We augmented that survey with surveys of rare trees, opportunistic collections from river valley and ravine habitats, herbarium collections, phylogenetic analyses of a subset of collections, and observations submitted to online nature-reporting applications. We present ITS sequence barcode data for 33 species, phylogenetic analyses for Candelariaceae, Endocarpon, Flavopunctelia, the Lecanora dispersa group, Lecidella, Peltigera, Physconia, and Punctelia, and detailed descriptions of 114 species in 47 genera and 23 families. Two species are hypothesized to be new to North America (Endocarpon aff. unifoliatum, Lecidella albida), twelve more are new to Alberta (Amandinea dakotensis, Bacidia circumspecta, Candelaria pacifica, Candelariella antennaria, Heterodermia japonica, Lecania naegelii, Lecanora sambuci, Lecanora stanislai, Lecidea erythrophaea, Peltigera islandica, Phaeocalicium aff. tremulicola, and the introduced Xanthoria parietina), and five are putative new species to science (Physcia aff. dimidiata, Physcia aff. stellaris, Phaeocalicium sp., Phaeocalicium aff. tremulicola, Lichenaceae sp.). Illustrations are provided for all species to aid in verification and public outreach. Species richness was highest in foliose lichens (48), followed by crustose and calicioid lichens and allied fungi (41), with the lowest richness in fruticose lichens (25). We did a preliminary assessment of the suitability of species for citizen-science biomonitoring by assessing their distribution across the city, perceptibility to the public, identification accuracy, and, for a subset, how consistently species were surveyed by trained novices. Compared to other urban areas where lichen diversity has been studied, Edmonton is relatively species-rich in calicioids and Peltigera. Promising bioindicators may be limited to chlorolichens, including Caloplaca spp., Evernia mesomorpha, Flavopunctelia spp., Phaeophyscia orbicularis, Physcia adscendens, Physcia aipolia group, Physcia aff. stellaris, Usnea spp., and Xanthomendoza fallax. Other genera that may be responsive to pollutants such as Cladonia and Peltigera were almost exclusively restricted to river valley and ravine ecosystems, limiting their application as bioindicators. Some species commonly used as biomonitors elsewhere were too rare, small, poorly developed, or obscured by more common species locally (e.g., Candelaria concolor s.l., Xanthomendoza hasseana). The low overlap with lists of biomonitoring species from other regions of North America illustrates the necessity of grounding monitoring in knowledge of local diversity. Future augmentation of this list should focus on enhanced sampling of downed wood-, conifer-, and rock-dwelling lichens, particularly crustose species. The next step in developing a biomonitoring program will require modelling species' responses to known air quality and climatic gradients.

opencc-zeroSep 2022View details →

Concatenated amino acid (AA) phylogenetic dataset of nuclear gene orthologs for Ephydroidea (Diptera)

The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. Extraordinary diversity in life histories, feeding habits, and morphology are hallmarks of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm the placement of Cryptochetidae as a sister taxon to a large clade containing both Drosophilidae and Braulidae – the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.

opencc-zeroOct 2022View details →

The dataset of five chloroplast regions used in: A contribution to Gymnosphaera (Cyatheaceae) in mainland Asia: Two new species, reinstatement of Cyathea bonii, and their phylogenetic positions

Gymnosphaera represents a minor lineage within the scaly tree-fern family Cyatheaceae. Tropical and subtropical mainland Asia is a main distribution area of Gymnosphaera. However, the species diversity of Gymnosphaera is currently incompletely known in mainland Asia due to lacking critical revision. Here we present new findings of species diversity and their relationships with mainland Asian Gymnosphaera based on field surveys, the examination of herbarium collections, and phylogenetic analyses of sequences of multiple chloroplast and nuclear regions. Two new species, G. saxicola from southwestern Yunnan and G. bachmaensis from central Vietnam are established. Traditionally recognized G. podophylla is revealed to be a complex, from which G. bonii is reinstated as a distinct species. Our phylogenetic analyses identified four clades within Gymnosphaera in mainland Asia: G. denticulata clade, G. gigantea clade, G. podophylla clade, and G. salletii clade. The new species G. saxicola, which is special for its saxicolous habitat, was resolved as a sister to G. austroyunnanensis in the G. salletii clade. The newly discovered G. bachmaensis, which is characterized especially by the spathulate frond, was positioned in the G. podophylla clade, being sister to G. bonii. The mountainous region from south-central Vietnam northwards to western Yunnan is a diverse center of Gymnosphaera and more species of this group are probably to be discovered there.

opencc-zeroMay 2024View details →

Distribution dataset of the 140 Chinese mountain floras and dated phylogenetic tree

We compiled checklists of species of angiosperm for 140 Chinese mountain flora from previously published, comprehensive species checklists, white papers, and research papers. From our initial checklists, we excluded all nonnative species, and we reconciled taxonomy to the Leipzig Catalogue of Vascular Plants (LCVP), with infraspecific taxa combined under their respective species. Following taxonomic reconciliation and categorization within higher ranks, our dataset comprised a total of 17,576 species in 2,585 genera belonging to 251 families and 56 orders. In addition, six dated phylogenetic trees by the V.PhyloMaker2 approach are provided.

opencc-by-4.0Aug 2024View details →

Dataset and R code for 'Do Morphometric Data Improve Phylogenetic Reconstruction? A Systematic Review and Assessment'

Dataset of tree (.tre) files and R code for running generalized Robinson-Foulds distance (Smith, 2020a;b) analysis.  The .tre files can be read into R (R Core Team., 2023) using the ape::read.tree function (Paradis et al., 2003), full details in R code file.       Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290.  R Core Team. (2023). R: A Language and Environment for Statistical Computing. (Version 4.2.2). R Foundation for Statistical Computing, Vienna, Austria: https://www.R-project.org/.  Smith, M. R. (2020a). Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees. Bioinformatics, 36(20), 5007-5013. https://doi.org/10.1093/bioinformatics/btaa614  Smith, M. R. (2020b). TreeDist: distances between phylogenetic trees. R package version 2.7.0. doi:10.5281/zenodo.3528124.

opencc-by-4.0Jun 2023View details →

Megalothorax (Collembola: Neelidae): phylogenetic dataset and analysis files

Core dataset for the study of the tree of Megalothorax (Collembola, Neelidae).