I don't understand what you're trying to accomplish with the geom_line(), but your code works fine for me:

bdat <- read.table(sep="\t", quote="", stringsAsFactors = FALSE, header = TRUE, text = "clusters    hits    species
2 or more   100000  homo sapiens
3 or more   29411   homo sapiens
4 or more   14998   homo sapiens
5 or more   8655    homo sapiens
2 or more   250000  mus musculus
3 or more   100000  mus musculus
4 or more   56088   mus musculus
5 or more   32181   mus musculus
2 or more   100000  chimp
3 or more   30783   chimp
4 or more   14760   chimp
5 or more   8063    chimp
2 or more   2149    drosophila
3 or more   173 drosophila
4 or more   39  drosophila
5 or more   23  drosophila
2 or more   26402   Zebrafish
3 or more   7462    Zebrafish
4 or more   3557    Zebrafish
5 or more   2122    Zebrafish
2 or more   2757    C elegans
3 or more   409 C elegans
4 or more   115 C elegans
5 or more   56  C elegans
2 or more   243 Cerevisiae
3 or more   29  Cerevisiae
4 or more   8   Cerevisiae
5 or more   4   Cerevisiae
2 or more   25066   Zea mays
3 or more   2921    Zea mays
4 or more   940 Zea mays
5 or more   581 Zea mays
2 or more   3551    Arabidopsis thaliana
3 or more   482 Arabidopsis thaliana
4 or more   122 Arabidopsis thaliana
5 or more   43  Arabidopsis thaliana
")

ggplot(bdat, aes(x=hits, y = clusters,group = 1, colour = species)) + geom_point() + xlim(1000, 100000)
Warning message:
Removed 16 rows containing missing values (geom_point).

## Remove all data points <1000 and >100000 as they're not being plotted anyway
ggplot(bdat[bdat$hits>=1000 & bdat$hits<=100000,], aes(x=hits, y = clusters,group = 1, colour = species)) + geom_point() + xlim(1000, 100000) + geom_line()