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This dataverse contains datasets and scripts (R and Python) used in analyses and visualizations included in Young et al. "Conserved Transcriptomic Profiles Underpin Monogamy across Vertebrates." PNAS. 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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1 to 8 of 8 Results
Dec 11, 2018
Young, Rebecca, 2018, "Orthologous Gene Groups (OGGs) and their expression values", https://doi.org/10.18738/T8/CLHOFF, Texas Data Repository Dataverse, 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...
Dec 11, 2018
Young, Rebecca, 2018, "Species ecology and mating characteristics", https://doi.org/10.18738/T8/IWHEKH, Texas Data Repository Dataverse, V1
Ecological characteristics and mating system score for each species
Dec 11, 2018
Young, Rebecca, 2018, "Differential expression in monogamous versus non-monogamous species", https://doi.org/10.18738/T8/HFXGLP, Texas Data Repository Dataverse, V1, 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)
Dec 11, 2018
Young, Rebecca, 2018, "Novel candidates of monogamy in vertebrates", https://doi.org/10.18738/T8/8VMZB7, Texas Data Repository Dataverse, V1
Gene IDs, OGG group names, and Ensembl IDs for 24 novel candidate genes associated with monogamy across vertebrates
Dec 11, 2018
Young, Rebecca, 2018, "Clade-level orthologous gene groups", https://doi.org/10.18738/T8/7CPUFF, Texas Data Repository Dataverse, V1
Python code that subsets the OGGs with all clades into clade-specific OGGs and Ensembl IDs
Dec 11, 2018
Young, Rebecca, 2018, "Orthologous Gene Group processing and summary statistics", https://doi.org/10.18738/T8/9QV1QV, Texas Data Repository Dataverse, V1
--orthoMCL_ENS.html: 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. --MaxFinder_...
Dec 11, 2018
Young, Rebecca, 2018, "Differential expression analyses and novel candidate gene identification", https://doi.org/10.18738/T8/AMG5VD, Texas Data Repository Dataverse, V1
These scripts assess differential expression between monogamous and non-monogamous species between all clades and across evolutionary subgroupings. Different approaches to differential expression analysis were used to identify novel candidates associated with monogamy. --RRHO.htm...
Dec 11, 2018
Young, Rebecca, 2018, "Mating and ecological characteristics and their association with neural gene expression", https://doi.org/10.18738/T8/XYQVNU, Texas Data Repository Dataverse, V1
Scripts to compare within and between clade mating and ecological characteristics and their correlation with neural gene expression. --Eco_Mating_comparisonsHeatmaps.html: This markdown generates species and clade level ecology and mating system similarity heatmaps. --Expression_...
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