Origin and colonization time of the NZ populations
To infer the geographic origin of the D. pulicaria that invaded
South Island, genetic data are required from throughout the natural
range of this species. Although whole nuclear and mitochondrial genomes
are available for samples from North America and New Zealand, the only
data available for D. pulicaria from other continents are
mitochondrial CO1 gene sequences. For the maximum-likelihood tree using
mitochondrial CO1 gene sequences collected from D. pulicariaacross North America, South America, Europe, Asia, New Zealand, and the
north polar region, the South Island Daphnia clustered with a
subset of North American clones and a few clones from South America
(Fig. 3). Because South American D. pulicaria are thought to have
been introduced from North America (Crease et al. 2012), the phylogeny
suggests that the South Island Daphnia have a North American
origin.
To estimate when the South Island genotype diverged from North AmericanD. pulicaria , we calculated the nuclear genome-wide divergence
between synonymous sites for these two groups. The divergence time
between the South Island genotype and North American D. pulicaria(T1, Fig. 2) can be estimated by the average pairwise
distance of synonymous sites (d s) between North
American D. pulicaria and the South Island, NZ haplotypes
(d s = 0.00023). Letting T1 =d s /2·μ, with μ = 5.85 × 10−9being the mutation rate per site per generation (obtained from a
mutation-accumulation experiment; Keith et al. 2016), and assuming
~5 generations per year, we estimate that the South
Island genotype diverged from other North American D. pulicaria
~ 3400 years ago. Because the North IslandDaphnia have a hybrid origin, and we do not have genomic
sequences available for North American hybrids, the divergence time
between the North Island genotype and North American hybrids of D.
pulex × D. pulicaria cannot be estimated by this means.
We also estimated the expansion time of the South Island populations
(T2, Fig. 2). Assuming these populations descended from
a single primary colonization event, then the nucleotide diversity among
South Island haplotypes would have been acquired after the colonization,
and the expansion time can be estimated from the average synonymous
nucleotide divergence between the most distant population (Lake
Coleridge) and the remaining populations. We found that theDaphnia population from Lake Coleridge has an average of 24
synonymous substitutions (over a total of 7.05 million synonymous sites)
compared to the remaining populations, implying a expansion time of
T2 = d s /(2·μ) = 3.4 ×
10−6 / (2 × 5.85 × 10−9 / site /
generation × 5 generations / year) = ~58 years. This
calculation is supported by the presence of characteristic ephippia ofD. pulex/pulicaria in a sediment-dated core taken in Lake Hayes
that suggested appearance of this species in the lake in the late 1950s
or early 1960s (Samiulah Khan, pers. comm). Moreover, we found that the
North Island Daphnia has an identical ND5 nucleotide sequence and
only a single nucleotide difference on the COI gene relative to one of
the clones that invaded Japan between 680 and 3400 years ago (So et al.
2015), suggesting that these two have the same origin.