We mapped the distribution and diversity of mitochondrial D-loop haplotypes among 502 New Zealand house mice (Mus musculus). By widespread sampling from 74 sites, we identified 14 new haplotypes. We used Bayesian phylogenetic reconstructions to estimate the genetic relationships between the New Zealand representatives of Mus musculus domesticus (all six known clades) and M. m. castaneus (clade HG2), and mice from other locales. We defined four distinct geographic regions of New Zealand with differing haplotype diversity indices. Our Results suggest (a) two independent pre-1840 invasions by mice of different origin (domesticus clade E and castaneus clade HG2) at opposite ends of the country; (b) multiple later invasions by domesticus clades E and F accompanying the post-1840 development of New Zealand port facilities in the central regions, plus limited local incursions by domesticus clades A, B, C and D1; (c) a separate invasion of Chatham I. by castaneus clade HG2; (d) previously undescribed New Zealand haplotypes, potentially the products of localised indigenous mutation, and (e) hybridisation between different lineages.

The house mouse, Mus musculus , was first introduced into New Zealand in significant numbers in the early to mid nineteenth century, with genomic components from different sources of the three subspecies M. m. domesticus, M. m. musculus and M. m. castaneus. M. m. domesticus is now widely distributed in New Zealand, with genomic and morphological evidence of M. m. musculus in a few scattered locations. M. m. domesticus/M. m. castaneus hybrids are dominant in the southern third of the South Island. We anticipated that there should be a definable southern contact zone between pure M. m. domesticus and M. m. domesticus/M. m. castaneus hybrids. We tested this hypothesis by screening 170 DNA samples from mice collected in the southern South Island, using a PCR technique which rapidly distinguishes the mitochondrial genomes of the three subspecies. All mice sampled from in or north of Lincoln (43.63° S) had only M. m. domesticus mtDNA, whereas all those from or further south than Hook (44.68° S) had M. m. castaneus mtDNA Between the two sites, mice carrying mtDNA of both subspecies were found, sometimes in the same building. On present data, this contact zone extends approximately 50 km north to south and some 30 km inland. Classical tests with three nuclear DNA markers confirmed earlier work showing that the nuclear genomes of all mice appeared to be predominantly domesticus-like. We conclude that if purebred M. m. castaneus mice did originally reach New Zealand, extensive back-crossing with M. m. domesticus has made the castaneus nuclear genome virtually undetectable with the tests that we employ.

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

A robust rapid method is described for differentiating Mus musculus castaneus and domesticus sub-species based on the analysis of restriction fragment length polymorphisms in three regions of the mtDNA genome.