Datasets for "Analyses of expanded anchored-hybrid phylogenomic datasets support revisions to the higher classification of leafhoppers (Hemiptera: Cicadellidae)"
Dataset Description |
The following 5 files were used to reconstruct the phylogeny of the Membracoidea. 1. Taxon_sampling.csv: contains the sample IDs (1st column, used in the alignments) and the taxonomic information (2nd to 6th columns) for 269 samples. 2. concatenated_aa_.phy: a concatenated amino acid dataset with 52,987 amino acid positions. This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps. 3. concatenated_nt.phy: a concatenated nucleotide dataset with all codon positions included (158,961 nucleotide positions). This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps. 4. concatenated_12nt.phy: a concatenated nucleotide dataset with the third codon positions excluded (105,974 nucleotide positions). This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps. 5. 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. |
Subject |
Life Sciences |
Keywords |
Auchenorrhyncha; evolution; phylogeny; timetree |
License |
CC0 |
Funder |
U.S. National Science Foundation (NSF)-Grant:DEB-1639601 |
Funder |
National Natural Science Foundation of China-Grant:32370493, 32370495, 32170472 |
Corresponding Creator |
Yanghui Cao |
Downloaded |
4 times |
| Version | DOI | Comment | Publication Date |
|---|---|---|---|
| 2 | 10.13012/B2IDB-6904466_V2 | Taxon sampling was slightly modified and the contaminated sequences were removed at the request of the manuscript reviewers. | 2026-01-22 |
Contact the Research Data Service for help interpreting this log.
| RelatedMaterial | destroy: {"material_type"=>"Dataset", "availability"=>nil, "link"=>"https://doi.org/10.13012/B2IDB-6904466_V2", "uri"=>"10.13012/B2IDB-6904466_V1", "uri_type"=>"DOI", "citation"=>"Cao, Yanghui; Dietrich, Christopher H.; Dmitriev, Dmitry A.; Zou, Hongfen; Xue, Qingquan; Zhang, Yalin (2026): Datasets for \"Analyses of expanded anchored-hybrid phylogenomic datasets support revisions to the higher classification of leafhoppers (Hemiptera: Cicadellidae)\". University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-6904466_V2", "dataset_id"=>3281, "selected_type"=>"Dataset", "datacite_list"=>"IsNewVersionOf", "note"=>"", "feature"=>nil} | 2026-01-22T15:38:37Z |
| Dataset | update: {"all_globus"=>[nil, true]} | 2026-01-22T13:02:34Z |
| Dataset | update: {"all_medusa"=>[nil, true]} | 2026-01-22T00:55:09Z |
| Dataset | update: {"publication_state"=>["version candidate under curator review", "released"], "release_date"=>[nil, Thu, 22 Jan 2026]} | 2026-01-22T00:41:00Z |
| RelatedMaterial | update: {"note"=>[nil, ""]} | 2026-01-21T20:46:24Z |
| RelatedMaterial | update: {"link"=>["https://doi.org/10.13012/B2IDB-6904466_V1", "https://doi.org/10.13012/B2IDB-6904466_V2"], "citation"=>["Cao, Yanghui; Dietrich, Christopher H.; Dmitriev, Dmitry A.; Zou, Hongfen; Xue, Qingquan; Zhang, Yalin (2026): Datasets for \"Analyses of expanded anchored-hybrid phylogenomic datasets support revisions to the higher classification of leafhoppers (Hemiptera: Cicadellidae)\". University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-6904466_V1", "Cao, Yanghui; Dietrich, Christopher H.; Dmitriev, Dmitry A.; Zou, Hongfen; Xue, Qingquan; Zhang, Yalin (2026): Datasets for \"Analyses of expanded anchored-hybrid phylogenomic datasets support revisions to the higher classification of leafhoppers (Hemiptera: Cicadellidae)\". University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-6904466_V2"]} | 2026-01-21T08:56:38Z |
| Dataset | update: {"description"=>["The following 8 files were used to reconstruct the phylogeny of the Membracoidea.\r\n\r\n1. Taxon_sampling.csv: contains the sample IDs (1st column, used in the alignments) and the taxonomic information (2nd to 6th columns) for 269 samples.\r\n\r\n2. concatenated_aa_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_aa.phy. This file partitions the 53,094 amino acid positions into 427 character sets.\r\n\r\n3. concatenated_aa_.phy: a concatenated amino acid dataset with 53,094 amino acid positions. This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.\r\n\r\n4. concatenated_nt_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_nt.phy. This file partitions the 159,282 nucleotide positions into 427 character sets.\r\n\r\n5. concatenated_nt.phy: a concatenated nucleotide dataset with all codon positions included (159,282 nucleotide positions). This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.\r\n\r\n6. concatenated_12nt_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_nt.phy. This file partitions the 106,188 nucleotide positions into 427 character sets.\r\n\r\n7. concatenated_12nt.phy: a concatenated nucleotide dataset with the third codon positions excluded (106,188 nucleotide positions). This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.\r\n\r\n8. 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 50.\r\n", "The following 5 files were used to reconstruct the phylogeny of the Membracoidea.\r\n\r\n1. Taxon_sampling.csv: contains the sample IDs (1st column, used in the alignments) and the taxonomic information (2nd to 6th columns) for 269 samples.\r\n\r\n2. concatenated_aa_.phy: a concatenated amino acid dataset with 52,987 amino acid positions. This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.\r\n\r\n3. concatenated_nt.phy: a concatenated nucleotide dataset with all codon positions included (158,961 nucleotide positions). This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.\r\n\r\n4. concatenated_12nt.phy: a concatenated nucleotide dataset with the third codon positions excluded (105,974 nucleotide positions). This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps.\r\n\r\n5. 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.\r\n"]} | 2026-01-21T08:56:38Z |
| Dataset | update: {"hold_state"=>["version candidate under curator review", "none"]} | 2026-01-20T19:23:19Z |
| Dataset | update: {"version_comment"=>[nil, "Taxon sampling was slightly modified and the contaminated sequences were removed at the request of the manuscript reviewers."]} | 2026-01-18T08:57:10Z |
| RelatedMaterial | create: {"material_type"=>"Dataset", "availability"=>nil, "link"=>"https://doi.org/10.13012/B2IDB-6904466_V1", "uri"=>"10.13012/B2IDB-6904466_V1", "uri_type"=>"DOI", "citation"=>"Cao, Yanghui; Dietrich, Christopher H.; Dmitriev, Dmitry A.; Zou, Hongfen; Xue, Qingquan; Zhang, Yalin (2026): Datasets for \"Analyses of expanded anchored-hybrid phylogenomic datasets support revisions to the higher classification of leafhoppers (Hemiptera: Cicadellidae)\". University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-6904466_V1", "dataset_id"=>3281, "selected_type"=>"Dataset", "datacite_list"=>"IsNewVersionOf", "note"=>nil, "feature"=>nil} | 2026-01-18T08:53:11Z |
| Funder | create: {"name"=>"National Natural Science Foundation of China", "identifier"=>"", "identifier_scheme"=>"", "grant"=>"32370493, 32370495, 32170472", "dataset_id"=>3281, "code"=>"other"} | 2026-01-18T08:53:11Z |
| Funder | create: {"name"=>"U.S. National Science Foundation (NSF)", "identifier"=>"10.13039/100000001", "identifier_scheme"=>"DOI", "grant"=>"DEB-1639601", "dataset_id"=>3281, "code"=>"NSF"} | 2026-01-18T08:53:11Z |
| Creator | create: {"family_name"=>"Zhang", "given_name"=>"Yalin", "identifier"=>"0000-0002-1204-9181", "email"=>"yalinzh@nwsuaf.edu.cn", "is_contact"=>false, "row_position"=>6} | 2026-01-18T08:53:10Z |
| Creator | create: {"family_name"=>"Xue", "given_name"=>"Qingquan", "identifier"=>"0000-0003-4498-1114", "email"=>"xueqingquan_123@nwsuaf.edu.cn", "is_contact"=>false, "row_position"=>5} | 2026-01-18T08:53:10Z |
| Creator | create: {"family_name"=>"Zou", "given_name"=>"Hongfen", "identifier"=>"0000-0002-3292-0341", "email"=>"zouhongfen@nwafu.edu.cn", "is_contact"=>false, "row_position"=>4} | 2026-01-18T08:53:10Z |
| Creator | create: {"family_name"=>"Dmitriev", "given_name"=>"Dmitry A.", "identifier"=>"0000-0002-3293-4794", "email"=>"proceps@illinois.edu", "is_contact"=>false, "row_position"=>3} | 2026-01-18T08:53:10Z |
| Creator | create: {"family_name"=>"Dietrich", "given_name"=>"Christopher H.", "identifier"=>"0000-0003-4005-4305", "email"=>"chdietri@illinois.edu", "is_contact"=>false, "row_position"=>2} | 2026-01-18T08:53:10Z |
| Creator | create: {"family_name"=>"Cao", "given_name"=>"Yanghui", "identifier"=>"0000-0002-0515-0767", "email"=>"caoyh@illinois.edu", "is_contact"=>true, "row_position"=>1} | 2026-01-18T08:53:10Z |
| Dataset | update: {"corresponding_creator_name"=>[nil, "Yanghui Cao"], "corresponding_creator_email"=>[nil, "caoyh@illinois.edu"]} | 2026-01-18T08:53:10Z |