Datasets

Genetic marker data

Cattle breed microsatellites

• name: microbov
• source: package adegenet
• size: 704 genotypes, 30 microsatellites, 373 alleles

Here is some reproducible code to access the data:

library(adegenet)
data(microbov)
microbov

Cat colonies in Nancy (France)

• name: nancycats
• source: package adegenet
• size: 237 genotypes, 9 microsatellites, 108 alleles

Here is some reproducible code to access the data:

library(adegenet)
data(nancycats)
nancycats

Extended HGDP-CEPH panel (Human microsatellites)

• name: eHGDP
• source: package adegenet
• size: 1350 genotypes, 378 microsatellites, 8170 alleles

Here is some reproducible code to access the data:

library(adegenet)
data(eHGDP)
eHGDP

Landscape genomic data for loblolly pine (Pinus taeda L.) (SNP)

• source: website of Andrew Eckert: (http://eckertdata.blogspot.fr/)
• size: 550 trees in 94 counties; 1730 SNPs
• other data: Spatial coordinates and environmental data in each county

Alpine plants in the European Alps (AFLP)

• source: dryad (http://datadryad.org/resource/doi:10.5061/dryad.f3rk4)
• size: 27 species; total of 9039 individuals geo-localized in 3063 locations; 5377 AFLPs
• other data: Spatial coordinates available in Dryad ; environmental data (S. Manel) *references: Gugerli et al. (2008) PPES; Taberlet et al. (2012) Ecol Letters ; Meirmans et al. (2011) Mol Ecol

Genomic of Medicago truncatula (SNP)

• source: (http://www.medicagohapmap.org/)
• size: 262 Medicago truncatula accessions; SNPs
• Reference: Yoder et al. 2014 Genetics
• Comments: to organize if we use them

Bottlenose dolphin control region sequences and microsatellite loci

• name: dolph.seqs, dolph.msats
• source: package strataG
• size: 136 aligned 402 bp sequences, 15 loci typed for 126 samples

To access the data:

library(strataG)
data(dolph.seqs)
data(dolph.msats)
str(dolph.seqs)
str(dolph.msats)

# stratifications for individuals
data(dolph.strata)
str(dolph.strata)

Simulated Data

Landscape Range Expansion simulations of haploid SNPs adapting to an environmental cline

• This is a subset of the simulations used from Lotterhos and Whitlock 2015
• Datasets are from 4 demographic histories (Island model, isolation by distance, range expansion from 1 refuge, and range expansion from two refugia)
• Consist of 9900 neutral SNPs and 100 selected SNPs
• The landscape was sampled in various ways: (30, 60, or 90 locations) and (6, 20, or 60 individuals per location)
• https://github.com/DrK-Lo/2015LotterhosLandscapeSimsRandomData
• (All simulations used in paper are in Dryad repository)