An introduction LDna: Advanced

This vignette provides a tutorial that demonstrates the use of LDna on a RAD sequence landscape genomics data set from a Southeast Asian mosquito malaria vector, Anopheles baimaii. This species has a widespread distribution extending from Northeast India, through Myanmar and into Thailand. Prior polytene chromosome mapping studies suggests that one polymorphic inversion is found on each of the five chromosome arms (2L, 2R, 3L, 3R and the X-chromosome) in A. baimaii and that they constitute up to 43% of their respective chromosomes [1-3]. Intraspecific inversion polymorphism is expected to result in high LD between large sets of loci that are identified by LDna from population genomic data sets. The full RAD sequence data set consists of 3828 SNPs from 184 samples and 91 geographical sites but here we only use a random subset comprising 25% of these loci called r2.baimaii_subs. This tutorial assumes you have read and understood the LDna_basics tutorial, accessed through: vignette("LDna_basics", package="LDna").