Luckau Protocols:STRUCTURE

STRUCTURE

Tara K. Luckau's Home Page Conservation Genetics Lab Notebook Tara's Protocols

Purpose

The software program STRUCTURE is "a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations."

Protocol

• Structure 2.3.3 for MacOS

Formatting Data

MS Excel

• ROW 1 = marker names (structure term = "Marker Name")
  • since diploid, leave an extra column for the second allele between markers
• COLUMN 1 = sample names (structure term = "Label")
• COLUMN 2 = population designation (structure term = "PopData", in integer form)

Tara's thesis = county area

• • 1 = Camp Pendleton
  • 2 = Rancho Jamul / Hollenbeck
  • 3 = Point Loma / Cabrillo National Monument
  • 4 = Santa Ysabel Open Space Preserve
  • 5 = Torrey Pines State Natural Reserve
• COLUMN 3 = location designation (structure term = "LocData", in integer form)

Tara's thesis = array cluster

• • 1 = red cluster
  • 2 = green cluster
  • 3 = blue cluster
  • 

MS Word

• copy data from Excel, Paste Special into Word
  • as Unformatted Text
• Save As ...
  • Plain Text (.txt)
  • File Conversion: Latin-US (DOS), CR/LF

Structure

New Project

• File: New Project
• Step 1
  • Name the project: 20111106AXRJ
  • Select directory: Research/Structure/StructureDirectory
  • Choose data file: browse to the .txt file you just made (from Excel and Word)
• Step 2
  • Number of individuals: 93
  • Ploidy of data: 2
  • Number of loci: 10
  • Missing data value: 0
• Step 3
  • Row of marker names - check
  • Data file stores data for individuals in a single line - check
• Step 4
  • Individual ID for each individual - check
  • Putative population origin for each individual - check
  • Sampling location information - check

New Parameter Set

• Parameter Set: New...

• Run Length: 10,000 and 10,000
• Ancestry Model

Admixture

Independent (we expect allele frequencies in different populations to be reasonably different from each other; works well for many data sets (strong structure))

• Allele Frequency Model: Correlated (frequencies in the different populations are likely to be similar, due to migration or shared ancestry; improves clustering for closely related populations (subtle structure), but may increase the risk of overestimating K)
• Advanced: unclick "Compute probability of data (for estimating K)" to make program run faster

Run Project

• Parameter Set: Run

• K=1 through K=number of sampling sites

• to determine the most likely K,

Literature and Supporting Information

• Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959.
• Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587.
• Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7:574–578.
• Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9:1322–1332.