Introduction
The Daphnia pulex complex
contains at least eight genetically distinct species, widely found
throughout the northern hemisphere (Colbourne et al. 1998). Two of the
species, D. pulex and D. pulicaria , can form viable
hybrids, but are not easily distinguished morphologically, and typically
are identified by allozyme electrophoresis of the lactate dehydrogenase
locus, with homozygous D. pulicaria having two “fast” alleles
and homozygous D. pulex having two “slow” alleles (Hebert et
al. 1989; Crease et al. 2011). Hybrids with the heterozygous slow/fast
genotype are generally found in disturbed ponds or deforested areas
(Hebert et al. 1989). Due to the frequent gene flow between D.
pulex and D. pulicaria (Hebert et al. 1989; Cristescu et al.
2012), some hybrids are also homozygous for the Ldh locus, presumably
resulting from backcrossing with either D. pulex or D.
pulicaria (Xu et al. 2013), which further complicates the species
identification.
Both D. pulex and D. pulicaria can reproduce by cyclical
parthenogenesis (CP), with extended periods of parthenogenesis
interspersed with sexual resting-egg production (Hebert 1978; Hebert et
al. 1993). However, some clones in each species have lost the ability to
engage in meiosis and have become obligate parthenogens (OP) (Hebert and
Crease 1980; Hebert et al. 1993; Paland et al. 2005). Interestingly, the
loss of meiosis is often limited to females, and some OP D. pulexcan still produce functional males bearing haploid sperm. Such males
from OP D. pulex can mate with females from CP D. pulexand form viable hybrids, ~40% of which have the OP
phenotype (Innes and Hebert 1988), indicating that partially dominant
meiosis-suppressing elements are carried by OP males. Further analysis
has shown that all OP D. pulex share common haplotypes on
chromosomes VIII and IX that arose by introgression from D.
pulicaria (Xu et al. 2015) and are transmitted through OP males without
recombination (Tucker et al. 2013). These observations suggest that all
OP D. pulex may be descendants of a single hybridization event
between D. pulex and D. pulicaria. Initially, it was
thought that all F1 hybrids between D. pulex andD. pulicaria are obligate parthenogens (Crease and Lynch 1991),
but Heier and Dudycha (2009) found that F1 hybrids
between some CP D. pulex females and CP D. pulicaria males
have CP phenotypes and can backcross with both parental species and
themselves (Heier and Dudycha 2009). Thus, Xu et al. (2013) argued that
OP hybrids originated from a unique historical hybridization and
introgression event between female D. pulex and male D.
pulicaria .
Although asexual clones are generally thought to suffer from long-term
selective disadvantages resulting from reduced efficiency of purging
deleterious mutations (Lynch et al. 1993), the OP clones with hybrid
backgrounds from D. pulex and D. pulicaria are notably
invasive. For example, an obligately asexual D. pulex ×pulicaria hybrid clone invaded Africa after the 1920s (Mergeay et
al. 2006) and has spread throughout the range of native sexual D.
pulex and displaced the sexual population. This asexual hybrid
clone is thought to have been initially introduced from the USA via the
introduction of largemouth bass in 1927-29 and completely displaced all
other D. pulex genotypes in Africa within 60 years (Mergeay et
al. 2006). In addition, an OP D. pulex invasion in Japan,
involving four hybrid clones and thought to have happened between 680
and 3400 years ago, is unlikely due to human activity (So et al. 2015).
Recently, non-indigenous Daphnia species morphologically
determined to be from the D. pulex complex have been found in
several lakes on the South Island of New Zealand (NZ) (Duggan et al.
2012). Although Duggan et al. (2012) considered the invasive South
Island clones to be D. pulex, because their mitochondrial
cytochrome c oxidase subunit 1 (CO1) gene sequences formed a
monophyletic group with North American D. pulex , their
analysis only used a 658-bp fragment of CO1 nucleotide sequences from 7
South Island clones. Due to the frequent hybridization between D.
pulex and D. pulicaria (Hebert et al. 1989; Heier and Dudycha
2009; Cristescu et al. 2012), the mitochondrial genomes may actually
have either a D. pulicaria or D. pulex origin (Cristescu
et al. 2012; Marková et al. 2013). Although members of the South Island
populations are Ldh homozygotes (Duggan et al. 2012), it is unclear
whether this locus is homozygous for D. pulex or D.
pulicaria alleles, and again the interpretation may be clouded when
hybrids exist. Moreover, due to the limited sequencing information,
Duggan et al. (2012) were unable to estimate when the invasion occurred.
To obtain a better understanding of the NZ Daphniapulex/pulicaria invasion, we performed genome-wide analyses ofDaphnia pulex/pulicaria populations from 13 lakes across
the South Island and one lake on the North Island. The species
designations and likely sources of origin were determined via a survey
of D. pulicaria -specific markers and a whole-genomic phylogenetic
tree that includes D. pulicaria and D. pulex clones
collected across North America, Europe, and China.