Datasets for Phylogenomics of microleafhoppers (Hemiptera: Cicadellidae: Typhlocybinae): morphological evolution, divergence times and biogeography
Cite this dataset:
Cao, Yanghui; Dietrich, Christopher H.; Kits, Joel; Dmitriev, Dmitry A.; Xu, Ye; Huang, Min (2023): Datasets for Phylogenomics of microleafhoppers (Hemiptera: Cicadellidae: Typhlocybinae): morphological evolution, divergence times and biogeography. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8636195_V1
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Dataset Description

The following files were used to reconstruct the phylogeny of the leafhopper subfamily Typhlocybinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5.

1) Taxon_sampling.csv: contains the sample IDs (1st column) and the taxonomic information (2nd column). Sample IDs were used in the alignment files and partition files.

2) concatenated_nt_complete.phy: a complete concatenated nucleotide dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 154,992 nucleotide positions (intron included) from 665 loci. Hyphens are used to represent gaps.

3) concatenated_nt_complete_partition.nex: the partitioning schemes for concatenated_nt_complete.phy. The file partitions the 154,992 nucleotide characters into 426 character sets, and defines the best substitution model for each character set.

4) concatenated_cds_complete.phy: a complete concatenated coding DNA sequence dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 153,525 nucleotide positions (intron excluded) from 665 loci. Hyphens are used to represent gaps.

5) concatenated_cds_complete_partition.nex: the partitioning schemes for concatenated_cds_complete.phy. The file partitions the 153,525 nucleotide characters into 426 character sets, and defines the best substitution model for each character set.

6) concatenated_nt_reduced.phy: a reduced concatenated nucleotide dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 95,076 nucleotide positions (intron included) from 374 loci. Hyphens are used to represent gaps.

7) concatenated_nt_reduced_partition.nex: the partitioning schemes for concatenated_nt_reduced.phy. The file partitions the 95,076 nucleotide characters into 312 character sets, and defines the best substitution model for each character set.

8) concatenated_aa_complete.phy: a complete concatenated amino acid dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12, corresponding to concatenated_cds_complete.phy. The file lists the sequences of 248 samples with 51,175 amino acid positions from 665 loci. Hyphens are used to represent gaps.

9) concatenated_aa_complete_partition.nex: the partitioning schemes for concatenated_aa_complete.phy. The file partitions the 51,175 amino acid characters into 426 character sets, and defines the best substitution model for each character set.

10) concatenated_aa_reduced.phy: a reduced concatenated amino acid dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12, corresponding to concatenated_nt_reduced.phy. The file lists the sequences of 248 samples with 31,384 amino acid positions from 374 loci. Hyphens are used to represent gaps.

11) concatenated_aa_reduced_partition.nex: the partitioning schemes for concatenated_aa_reduced.phy. The file partitions the 31,384 amino acid characters into 312 character sets, and defines the best substitution model for each character set.

12) Individual_gene_alignment.zip: contains 426 FASTA files, each one is an 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 Auchenorrhyncha, Cicadomorpha, Membracoidea, anchored hybrid enrichment
License CC0
Funder U.S. National Science Foundation (NSF)-Grant:DEB-1639601
Corresponding Creator Yanghui Cao
Downloaded 128 times
Version DOI Comment Publication Date
1 10.13012/B2IDB-8636195_V1 2023-01-01
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update: {"nested_updated_at"=>[nil, Mon, 31 Jul 2023 14:20:37.682273000 UTC +00:00]} 2024-01-03T18:23:59Z
update: {"publication_state"=>["file embargo", "released"]} 2023-01-01T09:00:06Z