If you look at the result of geno.table() for chromosome 8, you'll see that there are a bunch of markers with strange segregation patterns.
But even if you drop those, there are still some markers that seem unlinked to the rest of the chromosome, and one of those, "SLCL|SCAFFOLD_8_47238483", seems to be causing the big dip in the LOD curve.
Rather than try to re-build the map entirely from scratch, I'd focus on omitting the markers that don't fit at all, and maybe re-mapping them if you can find a good place for them.
karl
library(qtl)
x <- read.cross("csvs", "", "pop2_geno-2135-markers.csv", "pop2_pheno.csv")
# prevent markers from being on top of each other
x <- jittermap(x)
# genome scan
x <- calc.genoprob(x, step=1, error.prob=0.002, map.function="kosambi")
out <- scanone(x, phe=2, method="hk")
plot(out)
# marker segregation on chr 8
geno.table(x, chr="8")
# drop markers deviating a great deal from 1:2:1
gt <- geno.table(x)
mar2drop <- rownames(gt)[gt$P.value < 0.01/nrow(gt)]
# re-run genome scan
x <- drop.markers(x, mar2drop)
x <- calc.genoprob(x, step=1, error.prob=0.002, map.function="kosambi")
out_rev <- scanone(x, phe=2, method="hk")
plot(out_rev)
# there's still a marker "SLCL|SCAFFOLD_8_47238483" which seems unlinked to surrounding markers
x <- drop.markers(x, "SLCL|SCAFFOLD_8_47238483")
x <- calc.genoprob(x, step=1, error.prob=0.002, map.function="kosambi")
out_rev2 <- scanone(x, phe=2, method="hk")
plot(out_rev2)