Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast PacificLink copied to clipboard!
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- Description:
- At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific. We used seascape genetic approaches to identify large-scale biogeographic population clusters and investigate whether they could be explained by oceanographic transport and other environmental drivers. We then modelled population genetic differentiation within clusters as a function of oceanographic transport and other environmental factors. Five geographic clusters were identified: Alaska/Canada, central California, continental Santa Barbara, California Channel Islands and mainland southern California/Baja California peninsula. The strongest break occurred between central and southern California, with mainland Santa Barbara sites forming a transition zone between the two. Breaks between clusters corresponded approximately to previously identified biogeographic breaks, but were not solely explained by oceanographic transport. An isolation-by-environment (IBE) pattern was observed where the northern and southern Channel Islands clustered together, but not with closer mainland sites, despite the greater distance between them. The strongest environmental association with this IBE pattern was observed with light extinction coefficient, which extends suitable habitat to deeper areas. Within clusters, we found support for previous results showing that oceanographic connectivity plays an important role in the population genetic structure of Macrocystis in the Northern hemisphere.
Usage Notes:Genotype Data_Structure format
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.Allelic Richness Code_standarich
R script for calculating standardized allelic richness using R package "standarich"Allelic Richness Data
Data file for calculating standardized allelic richness using R package "standarich"CCA Script
R script for performing canonical correspondence analysis for environmental data and Structure cluster membershipCCA Data
Data file for use with the CCA script for performing canonical correspondence analysis for environmental data and Structure cluster membership in RHabitat Network Script
R script for performing network analysis for summer transport time using R package "igraph"Habitat Network_OceanDistanceMatrices
Matrix of ocean transport distances for use with the Habitat Network ScriptHabitat Network_site_centers
Location data for use with the Habitat Network ScriptLinear Models Data
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.Linear Models - Central California
R script used to perform linear model selection for Central California populationsLinear Models - Santa Barbara Channel
R script used to perform linear model selection for Santa Barbara Channel mainland populationsLinear Models - Southern California
R script used to perform linear model selection for Southern California populationsGenetic Network Script - gtx2network
R script to construct a network based on Cavalli-Sforza chord distance between populations -
- Auteur(s) :
- Johansson, Mattias L., Alberto, FilipeUniversity of Windsor, Reed, Daniel C.University of Algarve, Raimondi, Peter T.University of California System, Coelho, Nelson C.University of Algarve, Young, Mary A.Cornell University, Drake, Patrick T.University of California, Santa Cruz, Edwards, Christopher A.University of California, Santa Cruz, Cavanaugh, KyleCornell University, Assis, JorgeUniversity of California Los Angeles, Ladah, Lydia B.University of Algarve, Bell, Tom W.Department of Biological Oceanography; CISESE; Ensenada C.P. 22860 Baja California México, Coyer, James A.University of California, Santa Barbara, Siegel, David A.Cornell Universityet Serrão, Ester A.University of California, Santa BarbaraUniversity of Algarve
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- Dépôt source:
- Dryad
- Éditeur(s):
- Dryad
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- Accès:
- Public
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- URL:
- http://datadryad.org/stash/dataset/doi:10.5061/dryad.gm2v0
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- Date de publication:
- 2015-09-03
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- Mots-clés (en):
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- Identificateur:
- https://doi.org/10.5061/dryad.gm2v0
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Référence bibliographique
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- Citation selon les normes APA:
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Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific. (2015). [Data set]. Dryad. http://datadryad.org/stash/dataset/doi:10.5061/dryad.gm2v0Référence copiée dans le presse-papier
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