Phylogeography and Population Genetics
In most populations, genetic diversities were not pronounced (Table 4;
Figure 2). A few COI haplotypes are particularly common, and the
majority of the other haplotypes differ by one or two mutations from one
of the common haplotypes in each population and lineage (Figure 2). Most
populations feature only a few COI haplotypes. This is the case
especially within lineages ICOI, IICOIand IIICOI as well as the populations of
IVCOI and VCOI along the Reykjanes
Ridge. A notable exception is population 1072 (lineage
VCOI) to the west of Iceland, where nine haplotypes were
observed. Nucleotide diversities were roughly an order of magnitude
larger in the ddRAD data compared to COI (Table 4). Statistics differed
slightly between the two datasets for populations and lineages in
IRAD, IIRAD, and IIIRAD,
but not extensively (see Table 4). Therefore, we will focus only on the
analyses of the dataset which included all five lineages.
Observed heterozygosity across all ddRAD sites was close to 0.1 for all
lineages and populations (Table 4). The level of inbreeding differed
among lineages. Within lineages
IRAD-IIIRAD and IVRAD,the inbreeding coefficient FIS was ≤ 0.14 for each
population, but 0.18 for VRAD (Table 4). Due to the
Wahlund effect, FIS increased when populations were
grouped into lineages IRAD, IIRAD and
IIIRAD, or all together (up to 0.27).
Most lineages appear to be geographically restricted and separated from
each other. Lineage ICOI is the most widely distributed
lineage ranging from the south-east to the north-east of Iceland around
a distance of 900 km. However, the population farthest into the Nordic
Seas (station 1159) is well-differentiated from the others with at least
five mutations separating the observed COI haplotype from all other
haplotypes (Figure 2). Among and within all lineages, populations are
strongly differentiated from each other. In the nuclear ddRAD data,
population differentiation within lineages is not well resolved in the
PCA and Structure analyses (Figure 3), however, the coancestry analyses
with fineRADstructure grouped most individuals by populations within
lineages, suggesting low but detectable levels of population
differentiation (Figure 3). Population differentiation is particularly
strong in COI, where the vast majority of populations are differentiated
by significant FST values larger than 0.7, often over
0.9 (Table 5). High and significant FST values were also
observed among several geographically close populations (<100
km apart), e.g. station 879 compared to 880 or 881. A few instances of
geographically distant but genetically similar populations in COI were
observed as well: 869 compared to 873 (210 km; lineage
ICOI), 880 and 881 compared to 1172
(~450 km; lineage ICOI), and to a lesser
degree 83 compared to 1072 (431 km; lineage VCOI) (Table
5). ddRAD FST values were lower with all values within
and among populations of lineages
IRAD-IIIRAD being ≤ 0.29 (Table 5).
Isolation-by-distance was observed in COI, though only a relatively
small fraction of the genetic differentiation was explained by
geographic distance (correlation coefficient rY1 = 0.56; p =
0.001; determination of genetic differentiation by geographic distance =
31.3 %), but not in the ddRAD data (correlation coefficient rY1 = 0.36;p = 0.15; determination of genetic differentiation by geographic
distance = 13.2 %). The high levels of genetic differentiation are
already observed at low geographic distances, which may explain the low
correspondence between genetic differentiation and geographic distance.
The discordance between mitochondrial and nuclear data impacts the
inferred geographic distribution of genetic lineages. It is noteworthy
that ICOI extends much farther to the north-east than
IRAD, whereas IICOI is much more
restricted to the near shelf of Iceland than IIRAD,
which extends farther to the east into the Arctic Ocean. The difference
at station 1219 is the most pronounced, which has been assigned to
IICOI, but in ddRAD appears to be a hybrid between
IRAD and IIIRAD, (Figure 2), which
otherwise occur farther south or north, respectively.
Demographic parameters (Tajima’s D and Fu’s Fs) are slightly negative
for most populations and lineages in COI. Notable exceptions are
IVCOI (Tajima’s D and Fu’s Fs positive) and
ICOI-IIICOI jointly analyzed (Fu’s Fs is
positive). In the nuclear data set, most single populations had positive
values close to zero (thus also lineages IVRAD and
VRAD), however, lineages IRAD,
IIRAD, IIIRAD and
IRAD-IIIRAD each had negative values
ranging from -0.13 to -0.59. The three EBSP analyses yielded slightly
diverging outcomes concerning the long-term trends. While in COI a
slightly decreasing population size over time was suggested, one of the
ddRAD-based EBSPs suggested long-term stability and the other a temporal
increase in population size. However, all three analyses suggest that
population sizes were strongly reduced shortly before the present
followed by a rapid recovery of population sizes, likely an expansion
following a bottleneck (Figure 5). It is difficult to estimate when this
bottleneck may have occurred due to the lack of a conclusive specific
substitution rate for isopods.