Nuclear (SNP) genotypes at 23 loci, gender, ploidy level, and mitochondrial
haplotype information for Potamopyrgus antipodarum snails from 16 New Zealand
lake populations.
SNP genotypes were obtained with Mass Array® iPLEX® assay consisting of 32 loci.
9 loci were not included in the analyses, because of too many missing data. The
names of these loci are listed below. SNP assay information can be found in The
Single Nucleotide Polymorphism Database (dbSNP)
(http://www.ncbi.nlm.nih.gov/snp) NCBI_ss numbers: 804270584-804270615.
Gender (male, female) was determined for each snail using dissecting microscope.
Males were distinguished from females by a presence of a penis.
Ploidy level was determined by flow cytometry.
The sequence alignment of mitochondrial haplotypes is provided in a separate file.
We confined our analyses to the 414 unique genotype/ploidy/mitochondrial haplotype
combinations in order to avoid biases arising from the treatment of genetically
identical individuals from the same lake (i.e., members of the same asexual lineage)
as independent data points. Column G (n_indentical_ind) lists the total number of
individuals with the same genotype/ploidy/mitochondrial haplotype combination
found.
Description of the column headings and abbreviations uded:
A - sample_name - unique name for each sample
B - lake - lake where the snails have been collected
C - habitat - all samples were collected in the shallow (0-1 m) littoral area of the lakes
with the exception of Lake Alexandrina, where the mid-water (1-3 m) and deep-water
(4-6 m) habitats were also sampled
D - gender - male (m), female (f), unknown (unkn)
E - ploidy - ploidy level: diploid (d), triploid (t), higher than triploid (r), unknown (unkn).
F - haplotype - mitochondrial haplotype names
G - n_identical - total number of individuals from the same lake with the same
genotype/ploidy/mitochondrial haplotype combination
H-AD - column names are SNP loci names. Genotypes at each locus are coded with
a double digit: Homozygotes are either 0101 or 0202, heterozygotes are 0102, and
missing data are 0000. It was not possible to reliably assign the identity of additional
alleles in polyploid individuals (e.g., to distinguish between genotypes AAB and
ABB).
Additional information to SNP genotype data:
The 9 loci not included in the analyses:
00021_0233
00158_0226
00809_0282
01423_0468
02215_0373
02445_0594
03631_1111
04262_1128
12778_0273
For the 23 loci included in the analyses, the alleles were re-coded as numbers.
The corresponding bases are listed below. The allele listed at first position after locus
name was re-coded as "01", second position as "02". Missing data are coded as "00".
00107_0203 G C
00237_0350 G T
00267_0539 C T
00380_0380 C A
00416_0188 C T
00435_0591 C
00544_0533 A G
00575_0495 T C
01194_0152 C T
01214_0241 G A
01359_1059 T C
01362_0231 A G
01458_0330 T C
01504_0434 C T
01653_0239 C T
01784_0435 C T
01956_0484 G A
02115_0447 T C
02167_0249 C A
02215_0373 T C
02882_0841 G A
03139_0442 T C
05210_0448 C T
12778_0273 C G
16882_0151 c T