Spatially varying selection amplifies intrapopulation differentiation among phenotypic traits in the rocky-shore mussel, Mytilus californianus
Data files
Jul 14, 2025 version files 1.18 MB
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adult.v.juv.csv
2.11 KB
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long-term-transplant-exp-tatoosh2023-2024.csv
3.28 KB
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M.californianus_juvenile_rec-transplant-tatoosh2023.csv
7.15 KB
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m.californianus_spatial_selection_code.R
17.71 KB
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README.md
7.46 KB
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rec_tran_hobo_dat.csv
868.14 KB
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SNVs_P14_P15_het_stats.csv
261.29 KB
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trait_data.csv
13.95 KB
Abstract
Strong ecological gradients along heterogeneous environments play an important role in shaping population differentiation across species ranges. Thus, the selective pressure of environmental variation on phenotypic variation strongly affects an organism’s ability to persist across diverse or new environments. We investigated the spatial variability of biological responses in the intertidal bivalve Mytilus californianus to highlight the costs and trade-offs of local adaptation and phenotypic plasticity across various functional traits in a dynamic environment, the marine intertidal. To test this, we performed a reciprocal transplant experiment with M. californianus individuals originating from the upper and lower intertidal measuring relevant phenotypic traits, followed by Whole Genome Sequencing (WGS). We determined that morphological traits in individuals demonstrated increased phenotypic plasticity when moved to new environments, whereas physiological traits such as metabolism had reduced plasticity. Additionally, mussels from high intertidal zones, which experience greater heat and aerial exposure stress, maintained lower metabolic rates and showed increased frequencies of non-synonymous mutations in functionally relevant heat shock proteins when compared to low intertidal mussels. These results suggest that morphological and physiological traits responded differently to spatially varying selection within the marine intertidal.
Dataset DOI: 10.5061/dryad.pnvx0k70n
Description of the data and file structure
Data was generated from reciprocal transplant experiments combined with next generation sequencing to identify intrapopulation genetic and phenotypic variation between M. californianus individuals positioned in the low and high intertidal.
Files and variables
File: rec_tran_hobo_dat.csv
Description: Temperature measurements were recorded in 5-minute intervals throughout the entire experimental period for both intertidal plots using Onset HOBO data loggers that were attached to anchored screw eyes positioned next to the experimental enclosures.
Variables
- Locale: Spatial position of hobo logger in the marine intertidal
- date: Date
- temp: Temperature in Celsius
- light: Amount of light detected from hobo logger. Not used in analyses.
File: M.californianus_juvenile_rec-transplant-tatoosh2023.csv
Description: Phenotypic traits from reciprocal transplant experiments between juvenile low and high mussels.
Variables
- Individual
- Indigenous Position
- Experimental Position
- Length: shell length (mm)
- Width: shell width (mm)
- Height: shell height (mm)
- Final Buoyancy Weight (g)
- Net Calcification: net calcification totals (g CaCO3)
- Calcification.Rate (g CaCO3 day−1)
- Weight in Air: total weight in air (g)
- Beginning Oxygen (mg O2)
- Ending Oxygen (mg O2)
- Change in Oxygen w/ correction
- Corrected Respiration w/ body weight (mg O2 g-1 h-1). Respiration rates were not collected for every individual used in the reciprocal transplant experiment. NAs correspond to these individuals.
- Control 1 Start (mg O2)
- Control 1 End (mg O2)
- Correction: Control 1 End - Control 1 Start
- Experiment Start time
- Experiment End time
- Date
File: adult.v.juv.csv
Description: Comparison of phenotypic traits between adult and juvenile mussels
Variables
- Indigenous Position
- Life Stage: adult or juvenile mussels
- Respiration Rate (mg O2 g-1 h-1)
- Calcification Rate (g CaCO3 day−1)
File: SNVs_P14_P15_het_stats.csv
Description: 638 SNVs that were used as our candidate SNVs in our population analysis and corresponding genetic diversity indices. S1, S5, S11, S13, P14, P15 correspond to the populations: Tatoosh Is. Low intertidal mussels used in reciprocal transplant experiment (P14), Tatoosh Is. High intertidal mussels used in reciprocal transplant experiment (P15); Snow Creek Boat Launch, WA (S1); Slip Point, WA (S5); Freshwater Bay, WA (S11); Port Townsend, WA (S13).
Variables
- chrom: Chromosome
- pos: Position on chromosome
- ref: Reference allele
- alt: alternative allele
- Annotation
- Annotation_Impact
- Gene_Name
- Transcript_BioType
- Description
- protein_id
- eggNOG annotation
- HGVS.c: variant in relation to the reference allele
- HGVS.p: predicted effect of variant on protein
- P14: Frequency of allele in the low intertidal individuals on Tatoosh Is.
- P15: Frequency of allele in the high intertidal individuals on Tatoosh Is.
- loading: Loading factor from PC1 (Appendix 4C)
- s1_Ho: observed heterozygosity
- s1_He: expected heterozygosity
- s1_pB: proportion of candidate SNVs
- s1_Fis: Inbreeding coefficient. Empty cells indicate there is zero genetic diversity in this population for this variant.
- s1_n: number of individuals
- s11_Ho: observed heterozygosity
- s11_He: expected heterozygosity
- s11_pB: proportion of candidate SNVs
- s11_Fis: inbreeding coefficient. Empty cells indicate there is zero genetic diversity in this population for this variant.
- s11_n: number of individuals
- s13_Ho: observed heterozygosity
- s13_He: expected heterozygosity
- s13_pB: proportion of candidate SNVs
- s13_Fis: inbreeding coefficient. Empty cells indicate there is zero genetic diversity in this population for this variant.
- s13_n: number of individuals
- s14_Ho: observed heterozygosity
- s14_He: expected heterozygosity
- s14_pB: proportion of candidate SNVs
- s14_Fis: inbreeding coefficient. Empty cells indicate there is zero genetic diversity in this population for this variant.
- s14_n: number of individuals
- s15_Ho: observed heterozygosity
- s15_He: expected heterozygosity
- s15_pB: proportion of candidate SNVs
- s15_Fis: inbreeding coefficient. Empty cells indicate there is zero genetic diversity in this population for this variant.
- s15_n: number of individuals
- s5_Ho: observed heterozygosity
- s5_He: expected heterozygosity
- s5_pB: proportion of candidate SNVs
- s5_Fis: inbreeding coefficient. Empty cells indicate there is zero genetic diversity in this population for this variant.
- s5_n: number of individuals
- Ht: overall heterozygosity
- Hs: average heterozygosity
- Fst: proportion of the total genetic variance
File: trait_data.csv
Description: Trait data of low and high intertidal individuals used in a reciprocal transplant experiment. For the non-experimental individuals (Treatment = N), only Respiration, Beg Length, Beg Width, Beg Height, and Beg Total Weight were collected for these individuals.
Variables
- Individual
- Treatment
- Indigenous Position
- Experimental Position
- Respiration Rate (mg O2 g-1 h-1). Respiration rates were not collected for every individual used in the reciprocal transplant experiment. NAs correspond to these individuals.
- Calcification Rate (g CaCO3 day−1)
- Growth Rate: measured as change in shell length (mm day−1)
- Beg Length: shell length (mm)
- Beg Width: shell width (mm)
- Beg Height: shell height (mm)
- Beg Total Weight: total weight measured as weight in air (g)
- Beg shell weight: shell weight estimated as the buoyant weight (g)
- Beg Tissue Weight: Beg Total weight - Beg shell weight. Refer to methods 2.3 Morphological Trait Measurements
- End Length: shell height (mm)
- End Width: shell width (mm)
- End Height: shell height (mm)
- Total Weight: total weight measured as weight in air (g)
- Age
- Actual Shell Weight: Refer to methods 2.3 Morphological Trait Measurements
- Tissue Weight: Total weight - Actual shell weight. Refer to methods 2.3 Morphological Trait Measurements
- Net Calcification (g CaCO3)
- Change in Width (mm day−1)
- Change in Height (mm day−1)
- Change in Total Weight (g day−1)
- Change in Shell Weight (g day−1)
- STI: Shell thickness index. Not used in analysis
File: long-term-transplant-exp-tatoosh2023-2024.csv
Description: Trait data from juveniles that were from the juvenile transplant experiment that were returned to their respective treatment plots for an additional 333 days
Variables
- Plot
- Indigenous Position
- Experimental Position
- Length: Shell length (mm)
- Width: Shell width (mm)
- Height: Shell height (mm)
- Buoyant weight (g)
- Weight in Air (g)
- Shell weight (g)
- Tissue weight (g)
- tissue total weight ratio: tissue weight/weight in air. Not used in analysis
File: m.californianus_spatial_selection_code.R
Description: Labeled code for all analyses performed.
Code/software
All analyses were conducted using the R statistical platform version 4.4.1 (R Core Team 2024).