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published: 2024-01-31
Wang, Xiudan; Dietrich, Christopher; Zhang, Yalin (2024): Datasets for Phylogeny and historical biogeography of leafhopper subfamily Coelidiinae (Hemiptera: Cicadellidae) based on morphological and molecular data . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5847605_V1
The included files were used to reconstruct the phylogeny of Coelidiinae using combined morphological and molecular data, estimate divergence times and reconstruct ancestral biogeographic areas as described in the manuscript submitted for publication. The file “Coelidiinae_dna_morph_combined.nex” is a text file in standard NEXUS format used by various phylogenetic analysis programs. This file includes the aligned and concatenated nucleotide sequences or five gene regions (mitochondrial COI and 16S, and nuclear 28S D-2, histone H3, histone H2A and wingless) indicated by standard “ACGT” nucleotide symbols with missing data indicated by “?”, and morphological character data as defined in Table S3 used in the analyses. The data partitions are indicated toward the end of the file by ranges of numbers (“charset Subset 1 – 4” for the DNA data and “charset morph” for the morphological characters) followed by commands for the phylogenetic analysis program MrBayes that specify the model settings for each data partition. Detailed data on species included (as rows) in the dataset, including collection localities and GenBank accession numbers are provided in the Table_S1_Specimen_information.csv file. The file "TablesS2-S4.pdf" lists the primers used for polymerase chain reaction amplification, the list of morphological character definitions, and the morphological character matrix. The file “RASP_Distribution.csv” contains a list of the species included in the phylogenetic dataset (first column) and a code (second column) indicating their distributions as follows: (A) Oriental, (B) Palaearctic, (C) Australian, (D) Afrotropical, (E) Neotropical, and (F) Nearctic. More than one letter indicates that the species occurs in more than one region. The file "infile_for_BEAST.txt" is the input file in XML format used for the molecular divergence time analysis using the program BEAST (Bayesian Evolutionary Analysis by Sampling Trees) as described in the Methods section of the manuscript. This file includes comments that document the steps of the analysis.
keywords:
leafhopper; phylogeny; DNA sequence; insect; timetree; biogeography
published: 2024-02-25
Coshic, Kush; Maffeo, Christopher; Winogradoff, David; Aksimentiev, Aleksei (2024): Select trajectories, simulation setup, and analysis for "The structure and physical properties of a packaged bacteriophage particle". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4930709_V1
Simulation trajectory data and scripts for Nature manuscript "The structure and physical properties of a packaged bacteriophage particle" that reports the all-atom structure of a complete HK97 virion, including its entire 39,732 base pair genome, obtained through multi-resolution simulations.
keywords:
Virus capsid; Bacteriophage packaging; Multiresolution simulations; all-atom MD simulation
published: 2023-12-19
Bush, Daniel; Calla, Bernarda; Berenbaum, May (2023): Data for "An Aspergillus Strain from Bee Bread of the Western Honey Bee (Apis mellifera) Displays Adaptations to Distinctive Features of the Hive Environment". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7212497_V1
Data for the Appendices of Bush et al. article published in Ecology and Evolution. Contains genomic analysis information for a strain of Aspergillus flavus isolated from bee bread in East Central Illinois.
keywords:
Excel; UIUC; Evolution and Ecology; Aspergillus flavus; genome
published: 2024-02-15
Hoggatt, Meredith; Starbuck, Clarissa; O'Keefe, Joy (2024): Data for "Acoustic monitoring yields informative bat population density estimates". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7001459_V1
Dataset includes the dataset for estimating bat density from acoustic data and the R code. The data support a publication by Meredith L. Hoggatt, Clarissa A. Starbuck, and Joy M. O'Keefe entitled Acoustic monitoring yields informative bat population density estimates.
keywords:
acoustics; bats; monitoring; population density; random encounter model
published: 2024-02-21
Hartman, Jordan H; Corush, Joel B; Larson, Eric R; Tiemann, Jeremy S; Willink, Philip; Davis, Mark A (2024): Data for "Niche conservatism and spread explain hybridization and introgression between native and invasive fish". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6979965_V1
Data associated with the manuscript "Niche conservatism and spread explain hybridization and introgression between native and invasive fish" by Jordan H. Hartman, Joel B. Corush, Eric R. Larson, Jeremy S. Tiemann, Philip Willink, and Mark A. Davis. For this project, we combined results of ecological niche models (ENMs) and next-generation restriction site-associated DNA sequencing (RADseq) to test theories of niche conservatism and biotic resistance on the success of invasion, hybridization, and extent of introgression between native Western Banded Killifish and non-native Eastern Banded Killifish. This dataset provides the sampling locations and number of Banded Killifish in each population, accession numbers for RADseq from the National Center for Biotechnology Information Sequence Read Archive and the assignment of each Banded Killifish, the habitat associations of each population from the ENMs, and the occurrence points used to build the ENMs.
keywords:
Banded Killifish; ecological niche model; Fundulus diaphanus; hybrid swarm; invasive species; Laurentian Great Lakes
published: 2024-01-19
Digrado, Anthony; Montes, Christopher; Baxter, Ivan; Ainsworth, Elizabeth (2024): Soybean seed quality response to eCO2 data files. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6453957_V2
This data set is related to a SoyFACE experiment conducted in 2004, 2006, 2007, and 2008 with the soybean cultivars Loda and HS93-4118. The experiment looked at how seed elements were affected by elevated CO2 and yield. In this V2, 2 new files were added per journal requirement. Total there are 5 data files in text format within the digrado_et_al_gcb_data_V2 and 1 readme file. The name of files are listed below. Details about headers are explained in the readme.txt file. <b>1. ionomic_data.txt file</b> contains the ionomic data (mg/kg) for the two cultivars. The file contains all six technical replicates for each plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>2. yield_data.txt file</b> contains the yield data for the two cultivars (seed yield in kg/ha, seed yield in bu/a, Protein (%), Oil (%)). The file contains yield data for every plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>3. mineral_pro_oil_yield.txt file</b> contains the yield per hectare for each mineral (g/ha) along with the yield per hectare for protein and oil (t/ha). This was obtained by multiplying the seed content of each element (minerals, protein, and oil) by the total seed yield. The file contains yield data for every plots. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>4. economic_assessment.txt file</b> contains data used to assess the financial impact of altered seed oil content on soybean oil production. <b>5. meteorological_data.txt file</b> contains the meteorological data recorded by a weather station located ~ 3km from the experimental site (Willard Airport Champaign). Data covering the period between May 28 and September 24 were used for 2004; between May 25 and September 24 were used in 2006; between May 23 and September 17 in 2007; and between June 16 and October 24 in 2008.
keywords:
protein; oil; mineral; SoyFACE; nutrient; Glycine max; soybean; yield; CO2; agriculture; climate change
published: 2023-12-01
Hohoff, Tara; Deppe, Jill (2023): Data for little brown occupancy and associated landcover data from McHenry County, Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0365076_V1
Mist netting data for little brown bats (Myotis lucifugus) in McHenry County, Illinois and output of acoustic data processed using Kaleidoscope (Version 5.1.9, Bats of North America 5.1.0; Wildlife Acoustics) auto-identification software. Associated survey metadata and landcover metrics calculated using Fragstats included.
keywords:
little brown bats; mist netting; acoustics
published: 2024-02-08
Martinez, Carlos; Pena, Gisselle; Wells, Kaylee K. (2024): "Prairie Directory of North America" (2013) Entries for the Tallgrass, Mixed Grass, and Shortgrass Prairie Regions of the United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0421892_V1
This dataset contains transcribed entries from the "Prairie Directory of North America" (Adelman and Schwartz 2013) for the Tallgrass, Mixed Grass, and Shortgrass prairie regions of the united states. We identified the historical spatial extent of the Tallgrass, Mixed Grass, and Shortgrass prairie regions using Ricketts et al. (1999), Olson et al. (2001), and Dixon et al. (2014) and selected the counties entirely or partially within these boundaries from the USDA Forest Service (2022) file. The resulting lists of counties are included as separate files. The dataset contains information on publicly accessible grasslands and prairies in these regions including acreage and amenities like hunting access, restrooms, parking, and trails.
keywords:
grasslands; prairies; prairie directory of north america; site amenities; site attributes
published: 2019-02-07
Nute, Michael; Yarlagadda, Karthik; Stumpf, Rebecca (2019): PICAN-PI Public Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1678505_V1
This dataset contains all data used in the two studies included in "PICAN-PI..." by Nute, et al, other than the original raw sequences. That includes: 1) Supplementary information for the Manuscript, including all the graphics that were created, 2) 16S Reference Alignment, Phylogeny and Taxonomic Annotation used by SEPP, and 3) Data used in the manuscript as input for the graphics generation (namely, SEPP outputs and sequence multiplicities).
keywords:
microbiome; data visualization; graphics; phylogenetics; 16S
published: 2019-03-06
Makhnenko, Roman; Tarokh, Ali (2019): Experimental data on bulk and unjacketed moduli of porous rocks. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7478121_V2
This dataset is provided to support the statements in Tarokh, A., and R.Y. Makhnenko. 2019. Remarks on the solid and bulk responses of fluid-filled porous rock, Geophysics. The unjacketed bulk modulus is a poroelastic parameter that can be directly measured in a laboratory test under a loading that preserves the difference between the mean stress and pore pressure constant. For a monomineralic rock, the measurement of the unjacketed bulk modulus is ignored because it is assumed to be equal to the bulk modulus of the solid phase. To examine this assumption, we tested porous sandstones (Berea and Dunnville) and limestones (Apulian and Indiana) mainly composed of quartz and calcite, respectively, under the unjacketed condition. The presence of microscale inhomogeneities, in the form of non-connected (occluded) pores, was shown to cause a considerable difference between the unjacketed bulk modulus and the bulk modulus of the solid phase. Furthermore, we found the unjacketed bulk modulus to be independent of the unjacketed pressure and Terzaghi effective pressure and therefore a constant.
keywords:
Poroelasticity; anisotropic solid skeleton; unjacketed bulk modulus; non-connected porosity
published: 2019-03-13
Ando, Amy; Fraterrigo, Jennifer; Guntenspergen, Glenn; Howlader, Aparna; Mallory, Mindy; Olker, Jennifer; Stickley, Samuel (2019): Spatial Conservation and Investment Portfolios to Manage Climate-Related Risk. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2887291_V1
keywords:
climate change; conservation; diversification; environmental investments; MPT; porftfolio; risk; uncertainty
published: 2019-03-22
Jones, Todd M.; Benson, Thomas J.; Ward, Michael P. (2019): Flight Ability of Juvenile Songbirds at Fledgling: Examples of Fledgling Drop Tests. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2044905_V1
This data publication provides example video clips related to research on association among flight ability of juvenile songbirds at fledging and juvenile morphological traits (wing emergence, wing length, body condition, mass, and tarsus length. File names reflect the species dropped in each video. These videos are supplemental material for scientific publications by the authors and reflect an example subset of all videos collected form 2017-2018 as part of a larger study on the post-fledging ecology of grassland and shrubland birds in east-Central Illinois, USA. No birds were harmed/injured in the production of these videos and procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 18221. Individuals depicted in the videos have given consent for the videos to be shared (talent/model release form; <a href="https://publicaffairs.illinois.edu/resources/release/">https://publicaffairs.illinois.edu/resources/release/</a>)
keywords:
songbirds; flight ability; wing development; wing length; wing emergence; nestling development; post-fledging
published: 2019-03-19
Molloy, Erin K.; Warnow, Tandy (2019): Data from: TreeMerge: A new method for improving the scalability of species tree estimation methods. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9570561_V1
This repository includes scripts and datasets for the paper, "TreeMerge: A new method for improving the scalability of species tree estimation methods." The latest version of TreeMerge can be downloaded from Github (https://github.com/ekmolloy/treemerge).
keywords:
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-16
Molloy, Erin K.; Warnow, Tandy (2019): Data from: Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0569467_V2
This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).<br /> <strong>List of Changes:</strong> • Updated timings for NJMerge pipelines to include the time required to estimate distance matrices; this impacted files in the following folder: <strong>data.zip</strong> • Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> • Added some additional information about the java command used to run ASTRAL-III; this impacted files in the following folders: <strong>data.zip; astral64-trees.tar.gz (new)</strong>
keywords:
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-10
Pradhan, Dikshant; Jensen, Paul (2019): Pradhan 2019 Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3352362_V1
Data necessary for production of figures presented in "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models" by Pradhan et al.
keywords:
Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models;
published: 2019-05-31
Krichels, Alexander (2019): Data for Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9733959_V1
This dataset includes all data presented in the manuscript entitled: "Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient"
keywords:
denitrification; depressions; microtopography; nitrous oxide; soil oxygen; soil temperature
published: 2019-06-03
Rando, Halie; Wadlington, William; Johnson, Jennifer; Stutchman, Jeremy; Trut, Lyudmila; Farré, Marta; Kukekova, Anna (2019): Red Fox (Vulpes vulpes) Y-Chromosome Sequence. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4447017_V1
This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.
keywords:
Y-chromosome; carnivore; Vulpes vulpes; sex chromosomes; MSY; Y-chromosome genes; copy-number variation; BCORY2; UBE1Y; next-generation sequencing
published: 2019-06-22
MacDonald, Sean; Ward, Michael; Sperry, Jinelle (2019): Manipulating social information to promote frugivory by birds on a Hawaiian Island. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9223847_V1
keywords:
conspecific attraction; fruit-eating bird; Hawaiian flora; playback experiment; seed dispersal; social information; Zosterops japonicas
published: 2018-01-03
Sweet, Andrew; Bush, Sarah; Gustafsson, Daniel; Allen, Julie; DiBlasi, Emily; Skeen, Heather; Weckstein, Jason; Johnson, Kevin (2018): Data from: host and parasite morphology influence congruence between host and parasite phylogenies. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2011663_V1
Concatenated sequence alignment, phylogenetic analysis files, and relevant software parameter files from a cophylogenetic study of Brueelia-complex lice and their avian hosts. The sequence alignment file includes a list of character blocks for each gene alignment and the parameters used for the MrBayes phylogenetic analysis. 1) Files from the MrBayes analyses: a) a file with 100 random post-burnin trees (50% burnin) used in the cophylogenetic analysis - analysisrandom100_trees_brueelia.tre b) a majority rule consensus tree - treeconsensus_tree_brueelia.tre c) a maximum clade credibility tree - mcc_tree_brueelia.tre The tree tips are labeled with louse voucher names, and can be referenced in Supplementary Table 1 of the associated publication. 2) Files related to a BEAST analysis with COI data: a) the XML file used as input for the BEAST run, including model parameters, MCMC chain length, and priors - beast_parameters_coi_brueelia.xml b) a file with 100 random post-burnin trees (10% burnin) from the BEAST posterior distribution of trees; used in OTU analysis - beast_100random_trees_brueelia.tre c) an ultrametric maximum clade credibility tree - mcc_tree_beast_brueelia.tre 3) A maximum clade credibility tree of Brueelia-complex host species generated from a distribution of trees downloaded from https://birdtree.org/subsets/ - mcc_tree_brueelia_hosts.tre 4) Concatenated sequence alignment - concatenated_alignment_brueelia.nex
keywords:
bird lice; Brueelia-complex; passerines; multiple sequence alignment; phylogenetic tree; Bayesian phylogenetic analysis; MrBayes; BEAST
published: 2018-04-05
Brown, Patrick (2018): Phaseolus GBS. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6255617_V1
GBS data from Phaseolus accessions, for a study led by Dr. Glen Hartman, UIUC. <br />The (zipped) fastq file can be processed with the TASSEL GBS pipeline or other pipelines for SNP calling. The related article has been submitted and the methods section describes the data processing in detail.
published: 2018-08-01
Clark, Lindsay V.; Lipka, Alexander E.; Sacks, Erik J. (2018): Scripts for testing the error rate of polyRAD. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9729830_V1
This set of scripts accompanies the manuscript describing the R package polyRAD, which uses DNA sequence read depth to estimate allele dosage in diploids and polyploids. Using several high-confidence SNP datasets from various species, allelic read depth from a typical RAD-seq dataset was simulated, then genotypes were estimated with polyRAD and other software and compared to the true genotypes, yielding error estimates.
keywords:
R programming language; genotyping-by-sequencing (GBS); restriction site-associated DNA sequencing (RAD-seq); polyploidy; single nucleotide polymorphism (SNP); Bayesian genotype calling; simulation
published: 2018-08-03
Kim, Eun Sun; Zaya, David N.; Fant, Jeremie B.; Ashley, Mary V. (2018): Castilleja coccinea fruit set and seed set data from Illinois Beach State Park . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0852856_V2
These data include information on a field experiment on Castilleja coccinea (L.) Spreng., scarlet Indian paintbrush (Orobanchaceae). There is intraspecific variation in scarlet Indian paintbrush in the color of the bracts surrounding the flowers. Two bract color morphs were included in this study, the scarlet and yellow morphs. The experiment was conducted at Illinois Beach State Park in 2012. The aim of the work was to compare the color morphs with regard to 1) self-compatibility, 2) response to pollinator exclusion, 3) cross-compatibility between the color morphs, and 4) relative female fertility and male fitness. Three files are attached with this record. The raw data are in "fruitSet.csv" and "seedSet.csv", while "readme.txt" has detailed explanations of the raw data files.
keywords:
Castilleja coccinea; Orobanchaceae; floral color polymorphism; bract color polymorphism; breeding system; hand-pollination; self-compatibility; reproductive assurance
published: 2018-11-21
Clark, Lindsay V.; Lipka, Alexander E.; Sacks, Erik J. (2018): Scripts for testing the error rate of polyRAD. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9729830_V2
This set of scripts accompanies the manuscript describing the R package polyRAD, which uses DNA sequence read depth to estimate allele dosage in diploids and polyploids. Using several high-confidence SNP datasets from various species, allelic read depth from a typical RAD-seq dataset was simulated, then genotypes were estimated with polyRAD and other software and compared to the true genotypes, yielding error estimates.
keywords:
R programming language; genotyping-by-sequencing (GBS); restriction site-associated DNA sequencing (RAD-seq); polyploidy; single nucleotide polymorphism (SNP); Bayesian genotype calling; simulation
planned publication date: 2024-12-01
Hohoff, Tara; Rogness, Brittany; Davis, Mark (2024): Forestry Management Survey by the Illinois Bat Conservation Program. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1426397_V1
Survey questions and data collected from Illinois land managers on practices and knowledge relating to impacts to wildlife. 0s indicated non-selection, 1s indicate selection of answer.
keywords:
forestry management; online survey; wildlife
published: 2019-08-13
Nowak, Jennifer E.; Sweet, Andrew D.; Weckstein, Jason D.; Johnson, Kevin P. (2019): Data for: A molecular phylogenetic analysis of the genera of fruit doves and their allies using dense taxonomic sampling. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9797270_V1
Multiple sequence alignments from concatenated nuclear and mitochondrial genes and resulting phylogenetic tree files of fruit doves and their close relatives. Files include: BEAST input XML file (fruit_dove_beast_input.xml); a maximum clade credibility tree from a BEAST analysis (fruit_dove_beast_mcc.tre); concatenated multiple sequence alignment NEXUS files for the novel dataset (fruit_dove_concatenated_alignment.nex, 76 taxa, 4,277 characters) and the dataset with additional sequences (fruit_dove_plus_cibois_data_concatenated_alignment.nex, 204 taxa, 4,277 characters), both of which contain a MrBayes block including partition information; and 50% majority-rule consensus trees generated from MrBayes analyses, using the NEXUS alignment files as inputs (fruit_dove_mrbayes_consensus.tre, fruit_dove_plus_cibois_data_mrbayes_consensus.tre).
keywords:
fruit doves; multiple sequence alignment; phylogeny; Aves: Columbidae