This dataverse contains datasets and scripts (R and Python) used in analyses and visualizations included in Young et al. 2019. "Conserved Transcriptomic Profiles Underpin Monogamy across Vertebrates." PNAS (https://www.pnas.org/content/116/4/1331.long) Briefly, this study compared fore- and mid-brain transcriptomes of reproductive males in monogamous and non-monogamous species pairs of Peromyscus mice, Microtus voles, passeroid birds, dendrobatid frogs, and Xenotilapia species of cichlid fishes. Fore- and mid-brain mRNA of reproductive males samples (n=3) were pooled and sequenced using an Illumina HiSeq 2500. Additional raw and processed data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE123301: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123301 Species (abbreviation used for datasets): Microtus ochrogaster (Moch) M. pennsylvanicus (Mpen) Peromyscus californicus (Pcal) P. maniculatus (Pman) Anthus spinoletta (As) Prunella modularis (Dp) Ranitomeya imitator (Ri) Oophaga pumilio (Op) Xenotilapia spilotera (Xspil) X. ornatipinnis (Xorna)
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11 to 20 of 46 Results
orthoMCL_ENS_update.pdf
orthoMCL_ENS_update.pdf
Jun 5, 2019 - Orthologous Gene Group processing and summary statistics
Adobe PDF - 138.0 KB - MD5: 20a479153b7705983967fe0f4d917d07
R script that (1) generate a data frame for each species with raw reads and read per million (RPMs) for genes assigned to an OGG, and (2) identify the number of genes that overlap within a clade and the number of OGGs that overlap between clades.
Differential expression in monogamous versus non-monogamous species
Jun 5, 2019
Young, Rebecca, 2018, "Differential expression in monogamous versus non-monogamous species", https://doi.org/10.18738/T8/HFXGLP, Texas Data Repository, V2, UNF:6:Z76y+AthWIZ8+C+gGQMfQg== [fileUNF]
--[evolutionary subgroup]_DESeq.csv: Differential expression of OGGs between monogamous/non-monogamous species for distinct evolutionary subgroups. Analyses were performed using DESeq2 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html)
allvert_DEseq.csv
Jun 5, 2019 - Differential expression in monogamous versus non-monogamous species
Comma Separated Values - 272.6 KB - MD5: 8b6bc05944a7192ab6dcf15afcdb1056
amniotes_DESeq.csv
Jun 5, 2019 - Differential expression in monogamous versus non-monogamous species
Comma Separated Values - 271.8 KB - MD5: e3ef535c6ce0366e4a7b583d8b95c2d0
mammals_DESeq.csv
Jun 5, 2019 - Differential expression in monogamous versus non-monogamous species
Comma Separated Values - 274.3 KB - MD5: 55e8268c07ad97ca9e475d6ef330b983
tetrapods_DESeq.csv
Jun 5, 2019 - Differential expression in monogamous versus non-monogamous species
Comma Separated Values - 271.7 KB - MD5: c51423294947584d5ff61994cab15354
Orthologous Gene Groups (OGGs) and their expression values
Dec 11, 2018
Young, Rebecca, 2018, "Orthologous Gene Groups (OGGs) and their expression values", https://doi.org/10.18738/T8/CLHOFF, Texas Data Repository, V1, UNF:6:zIUzNl1KhQQi8cPaQmTSRA== [fileUNF]
--refGroups_OrthoMCLoutput.txt: Orthologous Gene Groups (OGGs) identified by orthoMCL an ortholog calling software package (http://orthomcl.org/common/downloads/software/). Orthologous gene groups were generated for all proteins from available, closely-related reference proteomes...
ALLsp_refGroupsIDs
Dec 11, 2018 - Orthologous Gene Groups (OGGs) and their expression values
Plain Text - 82.9 KB - MD5: 4b6e043312bf40d0147ba3200919a0f3
the subset of OGGs that have membership in all four reference species
As_GalCounts
Dec 11, 2018 - Orthologous Gene Groups (OGGs) and their expression values
Plain Text - 621.6 KB - MD5: 9d18e9d007ac57f74350c41de853664e
As_OGG.tab
Dec 11, 2018 - Orthologous Gene Groups (OGGs) and their expression values
Tabular Data - 263.3 KB - 2 Variables, 7327 Observations - UNF:6:l2BwM6+MPeLvt+nZhZEheA==
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