Species identification of the Daphnia from New Zealand lakes
We sampled Daphnia populations from 13 lakes on the South Island
and one on the North Island, New Zealand (NZ) (Fig. 1; Table S1).Daphnia populations from each lake were determined to be D.
pulex /D. pulicaria sensu lato based on morphological
features (Benzie 2005; Ebert 2005), although genetic information is
required to distinguish the two species. To obtain preliminary genetic
information in a simple manner, we pooled all individuals (50-200) from
each lake for whole-genomic sequencing. Each population was sequenced to
an average depth of sequencing coverage of 86× (Table 1), involving more
than 100 million 150-bp reads per population. On average, 1.5 million
bi-allelic sites were identified for each population (Table 1).
To determine the species of Daphnia populations in NZ, we first
relied on the lactate dehydrogenase locus (Ldh), a commonly invoked
indicator for distinguishing D. pulex and D. pulicaria(Hebert et al. 1989; Crease et al. 2011). For this locus, non-hybridD. pulicaria have two “fast” allozyme alleles and non-hybridD. pulex have two “slow” allozyme alleles. The mobility
difference is caused by the substitution of glutamine in D. pulexto glutamic acid in D.
pulicariaat
position 229 of the amino-acid sequence (Crease et al. 2011). We found
that all the South Island Daphnia populations are monomorphic for
glutamic acid at position 229, suggesting that the South Island
populations are D. pulicaria . However, the North Island
population is heterozygous for position 229, suggesting that it has a
hybrid origin.
In addition to the Ldh locus, we identified 24,185 informative sites by
comparing 14 D. pulicaria and 42 D. pulex genomes (Table
S2), in which all D. pulicaria are monomorphic for one
nucleotide and all D. pulex are monomorphic for another
nucleotide (File S2). We found that all the South Island Daphniapopulations have >23,390 (97%) sites homozygous forD. pulicaria- specific nucleotides, while only 807 (3.3%) sites
are homozygous in the North Island population. Our result is consistent
with a D. pulicaria origin of the South Island Daphniapopulations, and a hybrid origin of the North Island population.
To further confirm the species of Daphnia in NZ, we constructed a
consensus maximum-likelihood (ML) tree using whole-genomic coding
sequences from 14 NZ populations, 14 D. pulicaria, and 42D. pulex clones collected across North America, Czech Republic,
and China (Table S2). Within this tree, the South Island populations
formed a monophyletic clade with all North American D. pulicariaclones, further supporting the view that the South Island populations
are D. pulicaria (Fig. 2). The North Island population is in a
clade with North American D. pulicaria and D. pulex , but
clusters with neither North American D. pulicaria nor D.
pulex (Fig. 2), confirming its hybrid origin. Unlike the situation for
nuclear data, for the ML tree based on full-length mitochondrial
genomes, D. pulex and D. pulicaria clones interlaced
outside of the NZ populations (Fig. S1). This discordant phylogeny
between the mitochondrial and nuclear genomes may represent historical
hybridization between the two species (Marková et al. 2013).