Dataset for Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)
Cite this dataset:
Cao, Yanghui; Dietrich, Christopher H.; Zahniser, James N.; Dmitriev, Dmitry A. (2022): Dataset for Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8842653_V2
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Dataset 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.

1) taxon_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.

2)concatenated_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.

3) concatenated_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.

4) concatenated_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.

5) concatenated_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.

6) concatenated_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.

7) concatenated_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.

8) individual_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.
Subject Life Sciences
License CC0
Funder U.S. National Science Foundation (NSF)-Grant:DEB-1639601
Funder U.S. National Science Foundation (NSF)-Grant:DEB-0841612
Corresponding Creator Yanghui Cao
Downloaded 150 times
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
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update: {"nested_updated_at"=>[nil, Mon, 04 Dec 2023 20:28:59.425050000 UTC +00:00]} 2024-01-03T18:24:01Z
update: {"title"=>["Datasets for \"Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)\"", "Dataset for Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)"]} 2022-03-01T16:39:45Z