Genetic bottleneck simulation and detection (Sciuridae)

Knowledge graph centered on Genetic bottleneck simulation and detection (Sciuridae) with 31 nodes and 109 connections. Top connected: Marmota flaviventris, Spruce, mark-recapture (Sciuridae), Populus, Populus tremuloides.

Method synopsis

Computer simulation of population genetic changes during bottlenecks using BOTTLESIM software combined with multiple analytical approaches to detect bottleneck signatures.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Bottlenecks and rescue effects in a fluctuating population of golden-mantled ground squirrels (<i>Spermophilus lateralis</i>) (2011), Conservation Genetics. Implementations in other papers (listed below) may differ.

1. Bottleneck simulation modeling
   Used BOTTLESIM to create simulated datasets based on founder population using number of alleles, allele frequencies, and population size from year of highest abundance prior to demographic bottleneck (1997). Ran model for 1,000 iterations assuming random mating, age of reproductive maturity = 1 year, expected longevity = 2 years, and 10% generation overlap
   Quantities: 1,000 simulation iterations, founder population based on 1997 data (62 genes)Duration: Computational simulation period covering 8 years (1997-2005)Conditions: Closed population simulation with no immigration
   Equipment: BOTTLESIM software

Typical Equipment

• BOTTLESIM software
• BOTTLENECK software
• FSTAT software
• GENEPOP software
• HP-RARE software

Output Measurements

• M-ratios
• heterozygote excess
• allelic diversity changes
• bottleneck detection probability

Papers Using This Protocol (1)

Species Studied With This Protocol