DOI: 10.5061/dryad.pnvx0k70n
title: Spatially varying selection amplifies intrapopulation differentiation among phenotypic traits in the rocky-shore mussel, Mytilus californianus

description: 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.
description: # Spatially varying selection amplifies intrapopulation differentiation
 among phenotypic traits in the rocky-shore mussel, Mytilus californianus
 Dataset DOI: [10.5061/dryad.pnvx0k70n](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](https://onlinelibrary.wiley.com/doi/10.1002/ece3.71641#ece371641-bib-0064)).