CNAP genome-wide fitness trade-off analysis (Brassicaceae)

Knowledge graph centered on CNAP genome-wide fitness trade-off analysis (Brassicaceae) with 41 nodes and 147 connections. Top connected: Ligusticum porteri, Arabidopsis, Boechera stricta, Boechera, Festuca.

Method synopsis

Conditional Neutrality-Antagonistic Pleiotropy analysis estimates realized selection coefficients and uses permutation tests to identify genome-wide patterns of fitness trade-offs across environments and episodes of selection.

Synthesized from method descriptions across 2 papers 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 — Strong selection genome-wide enhances fitness tradeoffs across environments and episodes of selection (2014), Evolution. The protocol was originally introduced by Genetic tradeoffs and conditional neutrality contribute to local adaptation (2013), Molecular Ecology. Implementations in other papers (listed below) may differ.

1. Genotype molecular markers
   Genotyped RILs at 164 polymorphic molecular markers including 62 microsatellite loci and 102 single nucleotide polymorphisms, with average spacing of 5.5 cM across the genome
   Quantities: 164 molecular markers total, average 5.5 cM spacingDuration: Not specifiedConditions: Laboratory conditions
   Equipment: molecular genotyping equipment
2. Calculate genome-wide Montana allele percentage
   For each RIL, calculated the percentage of genome with Montana parent alleles (MT%) across all 164 molecular markers to quantify genome-wide local adaptation
   Quantities: MT% calculated for each of 172 RILs based on 164 markersDuration: Computational analysisConditions: Laboratory/computational
   Equipment: computers, statistical software

Typical Equipment

• computers
• statistical software

Output Measurements

• selection coefficients
• fitness trade-offs
• allelic correlations

Papers Using This Protocol (2)

Species Studied With This Protocol