SUPPLEMENTARY APPENDIX S2
Re-analysis of previously published microsatellite data
In Kemppainen et al. (2009) it was shown (using microsatellites and the mitochondrial
cytochrome b gene) that, similarly to many other species with limited dispersal, populations
cluster by geographic location rather than ecotype. Here we complement the four-locus
microsatellite data set of Kemppainen et al. (2009) with diversity indices and AMOVA
(analysis of molecular variance). Two of the locations were the same as in this study (Bergen
and Kosterfjord) and the last one was a location with SS- and LM-ecotypes from south
Shetland (UK). The four loci were not associated with the ecotype showing that they are
neutral with respect to sheltered/exposed microhabitats (Kemppainen et al., 2009). Standard
diversity indices were calculated in GENEPOP on the Web (Raymond and Rousset, 1995),
version 4 and an AMOVA was implemented in ARLEQUIN, version 3.11 (Exoffier et al. 2005;
locus by locus AMOVA averaged over all loci, 1000 permutations). Due to some
heterozygote deficiencies most likely caused by null alleles (Kemppainen et al., 2009) the
AMOVA was run both on an uncorrected data set and one corrected for null alleles, using the
INA method (Chapuis and Estoup, 2007).
Results
The diversity indices from the analyses of a four-locus microsatellite data set from
Kemppainen et al. (2009) showed that in these (presumably neutral) DNA markers the SSand LM-ecotypes are equally variable (see Table S2.1). In addition the AMOVA showed that
when the data were grouped by ecotype the among-group variation was zero while 7.6 % of
the variation was explained between locations within ecotypes (Table S2.2). When the data
were grouped by location, 6.3% of the variation was explained among groups while some
variation (1.2 %) was also explained between ecotypes within each location. This is consistent
with the notion that SS- and LM-ecotypes represent intra-specific variation and have similar
overall phylogeographic histories.
REFERENCES
Chapuis MP, Estoup A (2007). Microsatellite null alleles and estimation of population
differentiation. Mol. Biol. Evol. 24:621-631.
Excoffier L, Laval G, Schneider S (2005). Arlequin ver. 3.0: An integrated software package
for population genetics data analysis. Evol Bioinform Online 1:47-50.
Kemppainen P, Panova M, Hollander J, Johannesson K (2009). Complete lack of
mitochondrial divergence between two species of NE Atlantic marine intertidal
gastropods. J Evol Biol 22:2000-2011.
Raymond M, Rousset F (1995). An exact test for population differentiation. Evolution
49:1280-1283.
Table S2.1. Population statistics of previously published microsatellite data (Kemppainen et al., 2009). Sample sizes (n), number of loci,
expected and observed heterozygosities (Hz) and average number of alleles (No. alleles) and their standard deviations (SD).
Population
n
nr. of loci Expected Hz Unbiased Hz SD Obs Hz
Obs Hz SD
No. alleles
No. alleles SD
Shetland LE (GB)
32
4
0.8317
0.0856
0.6191
0.0434
15.5
5.26
Shetland SS (GB)
32
4
0.829
0.0679
0.6094
0.0431
14
6.48
Koster LE (Sweden) 32
4
0.8125
0.0576
0.6661
0.0418
15.5
6.61
Koster SS (Sweden) 32
4
0.8141
0.0715
0.7641
0.0378
14.5
7.14
Bergen LE (Norway) 32
4
0.8453
0.0643
0.7278
0.0403
15.5
7.55
Bergen SS (Norway) 32
4
0.8278
0.0464
0.7104
0.0406
11.5
4.65
Table S2.2. Locus by locus AMOVA (avaraged over all loci) for a four locus microsatellite data set (Kemppainen et al., 2009). Results with null
allelle corrected data (the INA method; Chapuis & Estoup, 2007) within brackets.
Data grouped by ecotype
Sourse of variation
d.f.
Sum of squares
% variation
P
Among groups
1
3.09
0 (0)
1 (1)
Among populations within groups
4
41.1
7.58 (6.02)
<0.0001 (<0.0001)
Within populations
378
631
94.5 (95.6)
<0.0001 (<0.0001)
Total
383
675
Sourse of variation
d.f.
Sum of squares
% variation
P
Among groups
2
35.0
6.28 (5.06)
<0.0001 (<0.0001)
Among populations within groups
3
9.03
1.16 (0.936)
<0.005 (<0.0001)
Within populations
378
631
92.6 (94.0)
<0.0001 (<0.0001)
Data grouped by location
Total
383
675