Transcriptomic Underpinnings of Monogamy in Vertebrates

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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1 to 10 of 46 Results

Differential expression analyses and novel candidate gene identification Jun 5, 2019 Young, Rebecca, 2018, "Differential expression analyses and novel candidate gene identification", https://doi.org/10.18738/T8/AMG5VD, Texas Data Repository, V3 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...
VertDESeq_names Jun 5, 2019 - Differential expression analyses and novel candidate gene identification Plain Text - 4.7 KB - MD5: bf81dc984de92db76eb37ef2679516a6 Ensembl IDs, Orthologous Gene Group, and Gene Symbol for genes identified by all clade DESeq2 analysis
Novel candidates of monogamy in vertebrates Jun 5, 2019 Young, Rebecca, 2018, "Novel candidates of monogamy in vertebrates", https://doi.org/10.18738/T8/8VMZB7, Texas Data Repository, V2 Gene IDs, OGG group names, and Ensembl IDs for 24 novel candidate genes associated with monogamy across vertebrates
GeneIDs_NovelCandidatesV2.csv Jun 5, 2019 - Novel candidates of monogamy in vertebrates Comma Separated Values - 1.1 KB - MD5: a56906b69c5432c4f1fbde4ad6263ddd Gene IDs, OGG group names, and Ensembl IDs for 24 novel candidate genes associated with monogamy across vertebrates
Mating and ecological characteristics and their association with neural gene expression Jun 5, 2019 Young, Rebecca, 2018, "Mating and ecological characteristics and their association with neural gene expression", https://doi.org/10.18738/T8/XYQVNU, Texas Data Repository, V2 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_...
Expression_Mating_EvolutionCompaisons_PIC_update.pdf Jun 5, 2019 - Mating and ecological characteristics and their association with neural gene expression Adobe PDF - 170.9 KB - MD5: 8f2156ddb6bc3002afde1dcb81d9828c This markdown contains code to generate within clad comparisons (monogamous vs. non-monogamous) of expression and divergence time (euclidean distance), expression and mating charactaristics (euclidean distance), and phylogenetic independent contrast of expression PC1 and mating
DESeq2_update.pdf Jun 5, 2019 - Differential expression analyses and novel candidate gene identification Adobe PDF - 156.0 KB - MD5: 7cec61740bc2c7adda003b2749706af1 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...
novelcandidates_update.pdf Jun 5, 2019 - Differential expression analyses and novel candidate gene identification Adobe PDF - 154.5 KB - MD5: 85046e5674d8f0dc78d700af2ff4b5b8 Integrate Log2 fold difference, DESeq2 all vertebrates, and RRHO most up- and down-regulated genes to generte a heatmap of novel candidates
Orthologous Gene Group processing and summary statistics Jun 5, 2019 Young, Rebecca, 2018, "Orthologous Gene Group processing and summary statistics", https://doi.org/10.18738/T8/9QV1QV, Texas Data Repository, V2 --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_...
MaxFinder_ParalogTest_update.pdf Jun 5, 2019 - Orthologous Gene Group processing and summary statistics Adobe PDF - 150.2 KB - MD5: afbf4a09d852922c861a5769763e165e R script that finds the gene with the largest log2fold change for each clade (positive or negative)using the normalized RPM, filters the name of that gene and generates a data frame with OrthoGroup, MaxLFC, and raw counts for these representative genes/OGGs for each species. In a...

Differential expression analyses and novel candidate gene identification

Jun 5, 2019

Young, Rebecca, 2018, "Differential expression analyses and novel candidate gene identification", https://doi.org/10.18738/T8/AMG5VD, Texas Data Repository, V3

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...

VertDESeq_names

Jun 5, 2019 - Differential expression analyses and novel candidate gene identification

Plain Text - 4.7 KB -

Ensembl IDs, Orthologous Gene Group, and Gene Symbol for genes identified by all clade DESeq2 analysis

Novel candidates of monogamy in vertebrates

Jun 5, 2019

Young, Rebecca, 2018, "Novel candidates of monogamy in vertebrates", https://doi.org/10.18738/T8/8VMZB7, Texas Data Repository, V2

Gene IDs, OGG group names, and Ensembl IDs for 24 novel candidate genes associated with monogamy across vertebrates

GeneIDs_NovelCandidatesV2.csv

Jun 5, 2019 - Novel candidates of monogamy in vertebrates

Comma Separated Values - 1.1 KB -

Gene IDs, OGG group names, and Ensembl IDs for 24 novel candidate genes associated with monogamy across vertebrates

Mating and ecological characteristics and their association with neural gene expression

Jun 5, 2019

Young, Rebecca, 2018, "Mating and ecological characteristics and their association with neural gene expression", https://doi.org/10.18738/T8/XYQVNU, Texas Data Repository, V2

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_...

Expression_Mating_EvolutionCompaisons_PIC_update.pdf

Jun 5, 2019 - Mating and ecological characteristics and their association with neural gene expression

Adobe PDF - 170.9 KB -

This markdown contains code to generate within clad comparisons (monogamous vs. non-monogamous) of expression and divergence time (euclidean distance), expression and mating charactaristics (euclidean distance), and phylogenetic independent contrast of expression PC1 and mating

DESeq2_update.pdf

Jun 5, 2019 - Differential expression analyses and novel candidate gene identification

Adobe PDF - 156.0 KB -

novelcandidates_update.pdf

Jun 5, 2019 - Differential expression analyses and novel candidate gene identification

Adobe PDF - 154.5 KB -

Integrate Log2 fold difference, DESeq2 all vertebrates, and RRHO most up- and down-regulated genes to generte a heatmap of novel candidates

Orthologous Gene Group processing and summary statistics

Jun 5, 2019

Young, Rebecca, 2018, "Orthologous Gene Group processing and summary statistics", https://doi.org/10.18738/T8/9QV1QV, Texas Data Repository, V2

--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_...

MaxFinder_ParalogTest_update.pdf

Jun 5, 2019 - Orthologous Gene Group processing and summary statistics

Adobe PDF - 150.2 KB -

R script that finds the gene with the largest log2fold change for each clade (positive or negative)using the normalized RPM, filters the name of that gene and generates a data frame with OrthoGroup, MaxLFC, and raw counts for these representative genes/OGGs for each species. In a...

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