A newer version of this dataset is available.
View the latest version.
| Version | DOI | Comment | Publication Date |
|---|---|---|---|
| 2 | 10.13012/B2IDB-8842653_V2 | Updated files because a few species names were changed and uploaded two additional files "concatenated_nt_106taxa.phy" and "concatenated_nt_106taxa_partition.nex", which were included during the revision of the paper. | 2022-03-01 |
| 1 | 10.13012/B2IDB-8842653_V1 | 2022-03-01 |
Contact the Research Data Service for help interpreting this log.
| update: {"nested_updated_at"=>[nil, Mon, 28 Feb 2022 19:36:24.404144000 UTC +00:00]} | 2024-01-03T18:23:56Z |
| update: {"release_date"=>[nil, Tue, 01 Mar 2022], "publication_state"=>["file embargo", "released"]} | 2022-03-01T16:52:36Z |
| update: {"release_date"=>[Thu, 30 Jun 2022, nil]} | 2022-03-01T16:52:36Z |
| update: {"publication_state"=>["released", "file embargo"]} | 2022-02-28T19:36:26Z |
| update: {"publication_state"=>["file embargo", "released"]} | 2022-02-28T19:36:26Z |
| update: {"hold_state"=>["none", "files temporarily suppressed"]} | 2022-02-28T19:35:09Z |
| update: {"publication_state"=>["released", "file embargo"]} | 2022-02-28T15:37:00Z |
| update: {"publication_state"=>["file embargo", "released"]} | 2022-02-28T15:37:00Z |
| update: {"publication_state"=>["released", "file embargo"]} | 2022-02-27T22:57:11Z |
| update: {"publication_state"=>["file embargo", "released"]} | 2022-02-27T22:57:11Z |
| update: {"description"=>["The following files were used to reconstruct the phylogeny of the leafhopper subfamily Deltocephalinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5.\r\nTaxon_sampling.csv: contains the sequencing ids (1st column) and the taxonomic information (2nd column) of each sample. Sequencing ids were used in the alignment files and partition files. \r\nconcatenated_nt.phy: concatenated nucleotide alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file lists the sequences of 163,365 nucleotide positions from 429 genes in 730 samples. Hyphens are used to represent gaps.\r\nconcatenated_nt_partition.nex: the partitions for the concatenated nucleotide alignment. The file partitions the 163,365 nucleotide characters into 429 character sets, and defines the best substitution model for each character set.\r\nconcatenated_aa.phy: concatenated amino acid alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file gives the sequences of 53,969 amino acids from 429 genes in 730 samples. Hyphens are used to represent gaps.\r\nconcatenated_aa_partition.nex: the partitions for the concatenated amino acid alignment. The file partitions the 53,969 characters into 429 character sets, and defines the best substitution model for each character set.\r\nIndividual_gene_alignment.zip: contains 429 FAS files, one for each of the partitioned nucleotide character sets in the concatenated_nt_partition.nex file. 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", "The following files were used to reconstruct the phylogeny of the leafhopper subfamily Deltocephalinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5.\r\nTaxon_sampling.csv: contains the sequencing ids (1st column) and the taxonomic information (2nd column) of each sample. Sequencing ids were used in the alignment files and partition files. \r\nconcatenated_nt.phy: concatenated nucleotide alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file lists the sequences of 163,365 nucleotide positions from 429 genes in 730 samples. Hyphens are used to represent gaps.\r\nconcatenated_nt_partition.nex: the partitions for the concatenated nucleotide alignment. The file partitions the 163,365 nucleotide characters into 429 character sets, and defines the best substitution model for each character set.\r\nconcatenated_aa.phy: concatenated amino acid alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file gives the sequences of 53,969 amino acids from 429 genes in 730 samples. Hyphens are used to represent gaps.\r\nconcatenated_aa_partition.nex: the partitions for the concatenated amino acid alignment. The file partitions the 53,969 characters into 429 character sets, and defines the best substitution model for each character set.\r\nconcatenated_nt_106taxa.phy: a reduced concatenated nucleotide alignment representing 107 samples x 86 genes. This alignment is used to estimate the divergence times of Deltocephalinae using MCMCTree in PAML v4.9. The file lists the sequences of 79,239 nucleotide positions from 86 genes in 107 samples. Hyphens are used to represent gaps.\r\nconcatenated_nt_106taxa_partition.nex: the partitions for the nucleotide alignment concatenated_nt_106taxa.phy. The file partitions the 79,239 nucleotide characters into 86 character sets, and defines the best substitution model for each character set.\r\nIndividual_gene_alignment.zip: contains 429 FAS files, one for each of the partitioned nucleotide character sets in the concatenated_nt_partition.nex file. 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"]} | 2022-02-27T22:57:09Z |
| update: {"publication_state"=>["released", "file embargo"]} | 2022-02-24T16:22:58Z |
| update: {"publication_state"=>["file embargo", "released"]} | 2022-02-24T16:22:58Z |
| update: {"publication_state"=>["released", "file embargo"]} | 2021-11-11T20:10:09Z |
| update: {"publication_state"=>["file embargo", "released"]} | 2021-11-11T20:10:08Z |
| update: {"version_comment"=>[nil, ""], "subject"=>[nil, "Life Sciences"]} | 2021-11-11T20:10:07Z |