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.