Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific

Johansson ML, Alberto F, Reed DC, Raimondi PT, Coelho NC, Young MA, Drake PT, Edwards CA, Cavanaugh K, Assis J, Ladah LB, Bell TW, Coyer JA, Siegel DA, Serrão EA

Date Published: September 3, 2015

DOI: http://dx.doi.org/10.5061/dryad.gm2v0

 

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Title Genotype Data_Structure format
Description Complete genotype data in Structure program format. Row 1 lists the microsatellite markers. Microsatellite data are presented in two-column per marker format. Missing data are indicated with -9. Column 1 gives the population and sample identifier, column 2 gives the population number, remaining columns are microsatellite data.
Download Genotype Data_Structure format.txt (173.9 Kb)
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Title Allelic Richness Code_standarich
Description R script for calculating standardized allelic richness using R package "standarich"
Download Allelic Richness Code_standarich.R (17.40 Kb)
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Title Allelic Richness Data
Description Data file for calculating standardized allelic richness using R package "standarich"
Download Allelic Richness Data.txt (167.8 Kb)
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Title CCA Script
Description R script for performing canonical correspondence analysis for environmental data and Structure cluster membership
Download CCA Script.R (7.448 Kb)
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Title CCA Data
Description Data file for use with the CCA script for performing canonical correspondence analysis for environmental data and Structure cluster membership in R
Download CCA Data.txt (7.989 Kb)
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Title Habitat Network Script
Description R script for performing network analysis for summer transport time using R package "igraph"
Download Habitat Network Script.R (6.216 Kb)
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Title Habitat Network_OceanDistanceMatrices
Description Matrix of ocean transport distances for use with the Habitat Network Script
Download Habitat Network_OceanDistanceMatrices.mat (18.81 Mb)
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Title Habitat Network_site_centers
Description Location data for use with the Habitat Network Script
Download Habitat Network_site_centers.mat (2.377 Kb)
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Title Linear Models Data
Description Pairwise data for use with Linear Model R scripts. Includes comparison pair, Population In ID, Population Out ID, Groups to which Populations belong (SCA=Southern California, SBC=Santa Barbara Channel Mainland, CCA=Central California), Pairwise linearized FST (FST/1-FST), Distance between sites, Area of habitat between sites, Habitat area per km between sites, Summer and Winter mean temperature difference between sites, Summer and Winter mean maximum significant wave height, transport time (5km model), Annual, Seasonal, and Monthly minimum mean transport time between sites, and biomass correlation between sites using a 500m, 1000m, and 2000m buffer area around each site.
Download Linear Models Data.txt (301.2 Kb)
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Title Linear Models - Central California
Description R script used to perform linear model selection for Central California populations
Download Linear Models - Central California.R (15.15 Kb)
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Title Linear Models - Santa Barbara Channel
Description R script used to perform linear model selection for Santa Barbara Channel mainland populations
Download Linear Models - Santa Barbara Channel.R (16.45 Kb)
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Title Linear Models - Southern California
Description R script used to perform linear model selection for Southern California populations
Download Linear Models - Southern California.R (10.18 Kb)
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Title Genetic Network Script - gtx2network
Description R script to construct a network based on Cavalli-Sforza chord distance between populations
Download Genetic Network Script - gtx2network.R (4.653 Kb)
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When using this data, please cite the original publication:

Johansson ML, Alberto F, Reed DC, Raimondi PT, Coelho NC, Young MA, Drake PT, Edwards CA, Cavanaugh K, Assis J, Ladah LB, Bell TW, Coyer JA, Siegel DA, Serrão EA (2015) Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific. Molecular Ecology 24(19): 4866–4885. http://dx.doi.org/10.1111/mec.13371

Additionally, please cite the Dryad data package:

Johansson ML, Alberto F, Reed DC, Raimondi PT, Coelho NC, Young MA, Drake PT, Edwards CA, Cavanaugh K, Assis J, Ladah LB, Bell TW, Coyer JA, Siegel DA, Serrão EA (2015) Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.gm2v0
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