Data Set (knb-lter-sbc.73.4)

SBC LTER: Reef: Geospatial structure of microsatellite markers for the giant kelp, Macrocystis pyrifera, Santa Barbara CA, 2009

  Summary and Data Links People and Organizations Temporal, Geographic and Taxonomic Coverage Methods and Protocols  

These methods, instrumentation and/or protocols apply to all data in this dataset:

Protocols and/or Procedures
Description:

Methods are described in the paper:

Johansson, Mattias L, Raimondi, Peter T, Reed, Daniel C, Coelho, Nelson C, Serrão, Ester A, Alberto, Filipe A. In press. Looking into the black box: simulating the role of self-fertilization and mortality in the genetic structure of Macrocystis pyrifera. Molecular Ecology, 22:4842–4854.

Description:

Names of microsatellite marker loci are defined in the paper:

Alberto, F., A. C. Whitmer, N. C. Coelho, M. Zippay, E. Varela-Alvarez, P. T. Raimondi, D. C. Reed and E. A. Serrão. 2009. Microsatellite markers for the giant kelp Macrocystis pyrifera. Conservation Genetics. 10:1915-1917 doi: 10.1007/s10592-009-9853-9

Description:

R script to calculate summary statistics from microsatellite data

Script calculates mean number of alleles per locus, observed heterozygosity, expected heterozygosity, and Fis. Input files are microsatellite data only, with alleles separated into separate columns (i.e. 10 loci are presented in 20 columns, with no headers or other columns).

Software:
Implementation Info:
Distribution:
Available Online:
 View: http://sbc.lternet.edu/external/Reef/Data/Genomics/johansson_geospatial/Summary_Stats_Johansson.R
Version Number: 1
Description:

R script to simluate one generation of inbreeding

Script simulates selfing, and creation of full-sibling, half-sibling, and first cousins in proportions ranging from 0 to 100%. Input files are microsatellite data only, with alleles separated into separate columns (i.e. 10 loci are presented in 20 columns, with no headers or other columns).

Software:
Implementation Info:
Distribution:
Available Online:
 View: http://sbc.lternet.edu/external/Reef/Data/Genomics/johansson_geospatial/All_Crosses_20120824_Johansson.R
Version Number: 1