Illinois Data Bank - Dataset

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Datasets for "Phylogeny, Biogeography and Morphological Evolution of the Treehopper-Like Leafhoppers (Hemiptera: Cicadellidae) with Redefinition of Cicadellidae and Revised Status for Megophthalmidae and Ulopidae"
Cite this dataset:
Cao, Yanghui; Dietrich, Christopher H.; Dmitriev, Dmitry A.; Kits, Joel H.; Xue, Qingquan; Zhang, Yalin (2025): Datasets for "Phylogeny, Biogeography and Morphological Evolution of the Treehopper-Like Leafhoppers (Hemiptera: Cicadellidae) with Redefinition of Cicadellidae and Revised Status for Megophthalmidae and Ulopidae". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1475719_V1
Dataset Description

The following files were used to reconstruct the phylogeny of the Megophthalmidae and Ulopidae.
Taxon_sampling.csv: contains the sample IDs (1st column) which were used in the alignments and the taxonomic information (2nd to 6th columns).
concatenated_aa_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_aa.phy. This file partitions the 52,474 amino acid positions into 427 character sets.
concatenated_aa_.phy: a concatenated amino acid dataset with 52,474 amino acid positions. This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.
concatenated_nt_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_nt.phy. This file partitions the 158,364 nucleotide positions into 427 character sets.
concatenated_nt_.phy: a concatenated nucleotide dataset with 158,364 nucleotide positions. This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.
Individual_gene_alignment.zip: contains 427 FASTA files, each one represents the nucleotide alignment for a gene. Hyphens are used to represent gaps. These files were used to construct gene trees using IQ-TREE v1.6.12, followed by multispecies coalescent analysis using ASTRAL v 4.10.5 based the consensus trees with a minimum average bootstrap value of 70.

Subject Life Sciences
Keywords Cicadellidae; Classification; Phylogenomics; Megophthalminae; Ulopinae
License CC0
Release Date 2025-01-01
Funder U.S. National Science Foundation (NSF)-Grant:DEB-1639601
Funder National Natural Science Foundation of China-Grant:32370493, 32370495, 32170472
Funder Agriculture and Agri- Food Canada-Grant:J-001564, J-002279
Corresponding Creator Yanghui Cao
Version DOI Comment Publication Date
3 10.13012/B2IDB-1475719_V3 files added and updated to include more input files of analyses, related scripts, and the main outputs 2024-09-17
2 10.13012/B2IDB-1475719_V2 We updated our data matrices by excluding two samples and adding one new sample. 2024-08-16
1 10.13012/B2IDB-1475719_V1 2025-01-01
Files associated with this dataset will be made available 2025-01-01. Contact the Research Data Service with any questions.

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Dataset update: {"publication_state"=>["files permanently suppressed", "file embargo"]} 2024-08-16T15:17:03Z
Dataset update: {"publication_state"=>["file embargo", "files permanently suppressed"], "tombstone_date"=>[nil, Fri, 16 Aug 2024], "hold_state"=>["none", "files permanently suppressed"]} 2024-08-16T15:17:03Z
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Dataset update: {"publication_state"=>["released", "file embargo"]} 2024-05-03T20:34:17Z
Dataset update: {"publication_state"=>["file embargo", "released"]} 2024-05-03T20:34:17Z
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Dataset update: {"subject"=>["", "Life Sciences"]} 2024-05-03T20:34:16Z