Data from: Mate choice in the brain: Species differ in how male traits ‘turn on’ gene expression in female brains
Data files
May 21, 2024 version files 5.23 MB
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bedtools_gene_counts.gff
5.11 MB
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design.csv
2.43 KB
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Female_choice_behavior_data.csv
12.04 KB
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Female_trial_data.csv
12.73 KB
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Gene_Expression.TPS
81.04 KB
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Male_data.csv
6.78 KB
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README.md
6.74 KB
Abstract
Mate choice plays a fundamental role in speciation, yet we know little about the molecular mechanisms that underpin this crucial decision-making process. Stickleback fish differentially adapted to limnetic and benthic habitats are reproductively isolated and females of each species use different male traits to evaluate prospective partners and reject heterospecific males. Here, we integrate behavioral data from a mate choice experiment with gene expression profiles from the brains of females actively deciding whether to mate. We find substantial gene expression variation between limnetic and benthic females, regardless of behavioral context, suggesting general divergence in constitutive gene expression patterns, corresponding to their genetic differentiation. Intriguingly, female gene co-expression modules covary with male display traits but in opposing directions for sympatric populations of the two species, suggesting male displays elicit a dynamic genomic response that reflects known differences in female preferences. Furthermore, we confirm the role of numerous candidate genes previously implicated in female mate choice in other species, suggesting that evolutionary tinkering with these conserved molecular processes underlies divergent mate preferences and sexual isolation. Taken together, our study adds important new insights to our understanding of the molecular processes underlying female decision-making critical for generating sexual isolation and speciation.
https://doi.org/10.5061/dryad.ncjsxkt3g
Description of the data and file structure
We include in this submission all data required to run included code (see below for which order to run scripts):
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bedtools_gene_counts.gff
Tab delimited text file with rows corresponding to counts of genes for each sample. The first column is the Ensembl gene name.
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design.csv
Comma delimited text file with information for each female for which we have a transcriptome. It contains the following columns:
- female - female ID
- spawn - whether a female laid eggs (TRUE or FALSE)
- lake - female lake of origin (Paxton or Priest)
- species - female species (Limnetic or Benthic)
- treatment - experimental treatment (Het = heterospecific courtship, Con = conspecific courtship, Fem = social control)
- preference - courtship preference score (0-4); NA for Fem treatment because there was no courtship
- trial time - length of trial (MM:SS)
- batch - RNA extraction batch
- RIN - RNA RIN score from Agilent Bioanalyzer; NA if missing (e.g., due to instrument error)
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Female choice behavior data.csv
Comma delimited text file with behavioral information for each female that was in the behavioral experiments. It contains the following columns:
- File name - JWatcher file name
- Trial - trial number
- Trt Code - Concatenation of lake code, species code, and treatment code
- Lake - Lake code (Pa = Paxton, Pr = Priest)
- Species - Species code (L = Limnetic, B = Benthic)
- Trt - Treatment code (C = conspecific courtship, H = heterospecific courtship, F = social control)
- Sequenced - was the RNA sequenced? (Y/N)
- Date - date of behavioral trial (MDDYY)
- Obs - observer initials (all trials had two observers)
- Duration - duration of trial
- Follow - number of times female followed male when he did a lead
- Lead - number of times male tried to lead female
- Examine - number of times female examined a male’s nest
- Show - number of times a male showed a female his nest
- Male Approach - number of times a male approached a female
- Rub - number of times a male rubbed a female while she was in his nest
- Angle - number of times a female angled her body (a signal of interest)
- Female Approach - number of times a female approached a male
- Follow/Lead - proportion of leads where a female followed
- Examine/Show - proportion of shows where a female examined a nest
- Preference Score - preference score (0-4)
- Zigs - number of male zig-zag displays
- Bites - number of times male bit female
- Chases - number of times male chased female
- Enter - number of times female entered a male nest
- Spawn - number of times a male spawned in his nest
- Swims - number of movements that were greater than 1 body length
- Nesting - time (ms) male spent within one body length of his nest
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Female trial data.csv
Comma delimited text file with experimental trial information for each female for each trial in the behavioral experiments. It contains the following columns:
- Trial # - trial number
- Jwatcher file - JWatcher file name
- Date - date of behavioral trial (M/DD/YY)
- Time Start - time trial started (HH:MM)
- Trial Time - total trial time (MM:SS)
- Observer - observer initials
- Female Lake - female lake (Paxton or Priest)
- Female Species - female species (Limnetic or Benthic)
- Female Tank - female tank ID
- Male Lake - male lake (Paxton or Priest)
- Male Species - male species (Limnetic or Benthic)
- Nesting Tank - male nesting tank ID
- Treatment - treatment (Con Male = conspecific courtship, Het Male = heterospecific courtship, Female-Female = social control)
- Male Mark - male elastomer mark (R/L); 4 locations: h = head, d1 = front dorsal, d2 = back dorsal, t = tail; 2 colors: p = pink, w = white; in Female-Female trials no fish were marked so those cells are marked NA; null = mark should have been given but was not
- Comments - comments, if none the cell is left blank
- Surgery Time - time from fish decapitated to brain in tube of RNAlater (MM:SS); NA for mistrials where there was no surgery
- # Eggs - number of eggs; NA for mistrials where there was no surgery
- Female Picture Date - date female had photo taken; NA if missing
- Female Weight (g) - female weight (g); NA if missing
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Gene Expression.TPS
TPS file with landmark data used to generate size information.
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Male data.csv
Comma delimited text file with phenotypic information about each male for each trial in the behavioral experiments. It contains the following columns (NA indicates missing data):
- Trial Number - trial number
- Trial Date - date of behavioral trial
- Nesting Tank - male nesting tank ID
- Lake/ Species - lake of origin and species of male (Pax = Paxton, Mrs = Priest, B = Benthic, L = Limnetic)
- Home Tank - ID of tank male came from
- Mark - male elastomer mark (R/L); 4 locations: h = head, d1 = front dorsal, d2 = back dorsal, t = tail; 2 colors: p = pink, w = white
- Mark Date - date when male was marked
- Pheno Date - date when male was phenotypes
- Picture Date - date when male was photographed
- Weight - male weight (g)
- Throat Area - male throat area (0-5 with 1/2 point increments)
- Throat Int - male throat intensity (0-5 with 1/2 point increments)
- Eye Color - male eye color
- Eye Int - male eye color intensity (0-5 with 1/2 point increments)
- Body Color - male body color
- Body Int - male body color intensity (0-5 with 1/2 point increments)
- Body Drk - male body darkness (0-5 with 1/2 point increments)
- Spots - how many black spots did male have? (None, Few, Medium, Many, All over)
- Mottled? - did male have stripes? (Y/N)
Code/Software
To recreate our analyses and figures, execute the included code in the following order:
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Behavior and Morphology script.R
Script for quantifying and analyzing male and female behavior and morphology.
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DESeq2 script.R
Script for running gene expression analyses using DESeq2.
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WGCNA script.R, WGCNAscript2a1.R, WGCNAscript2a2.R
Scripts for running WGCNA.
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gprofiler script.R
Scripts for GO analyses of differentially expressed genes from #2 and modules from #3.