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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41 to 46 of 46 Results
BySpAllLifeHistory.txt
Dec 11, 2018 - Species ecology and mating characteristics
Plain Text - 521 B - MD5: 5e0def7a2d9f48cdcb23e56db6974176
Ecological characteristics and mating system score for each species
Clade-level orthologous gene groups
Dec 11, 2018
Young, Rebecca, 2018, "Clade-level orthologous gene groups", https://doi.org/10.18738/T8/7CPUFF, Texas Data Repository, V1
Python code that subsets the OGGs with all clades into clade-specific OGGs and Ensembl IDs
GetGroupNamesByIDs.py
Dec 11, 2018 - Clade-level orthologous gene groups
Unknown - 668 B - MD5: d740327a172d38dabc0f219d9bcfc309
subsets the OGGs with all clades into clade-specific OGGs and Ensembl IDs
OGGmeans_variance_CladeComparisons.html
Dec 11, 2018 - Orthologous Gene Group processing and summary statistics
HTML - 729.6 KB - MD5: a690d4e551e5a95804f2e0a10405670b
R script that calculates and compares overall patterns of relative expression of OGGs in monogamous and non-monogamous species across clades.
RRHO.html
Dec 11, 2018 - Differential expression analyses and novel candidate gene identification
HTML - 743.3 KB - MD5: 951fea3f943d8c740d2bd2df4dfd8612
R script that performs the Rank Rank Hypergeometric Overlap (RRHO) between all pairwise clades, generates lists of most up- and down-regulated OGGs, and generates the RRHO and summary plots.
Eco_Mating_comparisonHeatmaps.html
Dec 11, 2018 - Mating and ecological characteristics and their association with neural gene expression
HTML - 723.8 KB - MD5: 4a1d77c77dc113ef4c23ae1e446768dd
This markdown generates species and clade level ecology and mating system similarity heatmaps.
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