The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand

Abstract

The house mouse (Mus musculus) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human-mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus. We used the GigaMUGA genotyping array (approximately 135 000 loci) to describe the genomic ancestry of 161 mice, sampled from 34 locations from across New Zealand (and one Australian city—Sydney). Of these, two populations, one in the south of the South Island, and one on Chatham Island, showed complete mitochondrial lineage capture, featuring two different lineages of M. m. castaneus mitochondrial DNA but with only M. m. domesticus nuclear ancestry detectable. Mice in the northern and southern parts of the North Island had small traces (approx. 2–3%) of M. m. castaneus nuclear ancestry, and mice in the upper South Island had approximately 7–8% M. m. musculus nuclear ancestry including some Y-chromosomal ancestry—though no detectable M. m. musculus mitochondrial ancestry. This is the most thorough genomic study of introduced populations of house mice yet conducted, and will have relevance to studies of the isolation mechanisms separating subspecies of mice.

Phylogeography of Invasive Rats in New Zealand

“…The population genetics of house mice (Mus musculus) has been rigorously assessed across the New Zealand archipelago using a variety of genetic markers (Searle et al, 2009;King et al, 2016;Veale et al, 2018). The population genetics of R. exulans has also been assessed, as a proxy for Polynesian migration (Matisoo-Smith et al, 1998).…”

Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research

“…We have a long track record of developing genotyping arrays for the laboratory mouse, from the Mouse Diversity Array (MDA, Yang et al 2009 ) to the previous versions of the Mouse Universal Genotyping Array (MUGA) ( Morgan and Welsh 2015 ). These tools were originally designed for the genetic characterization of two popular genetic reference populations, the Collaborative Cross (CC) and the Diversity Outbred, and then used in experiments involving other laboratory strains as well as wild mice ( Yang et al 2011 ; Collaborative Cross Consortium 2012 ; Carbonetto et al 2014 ; Arends et al 2016 ; Didion et al 2016 ; Rosshart et al 2017 ; Shorter et al 2017 ; Srivastava et al 2017 ; Veale et al 2018 ).…”

Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri)

“…The small effective population size of mtDNA makes it more susceptible to the fixation of foreign haplotypes than nuclear DNA; consequently, introgression can be seen in mtDNA without any admixture in nuclear DNA [ 74 ]. In a recent genomic study of mice in New Zealand, for example, mitochondrial capture between subspecies was observed to have independently occurred in multiple populations with no detectable nuclear introgression [ 21 ].…”

“…Due to the complexity and high variability associated with genetic markers when examining population-level differences, mtDNA and nuclear DNA do not always show the same population structure, hence using both markers provides broader insight than using only one [ 2 ]. Hybridisation with red-billed gulls has previously been observed [ 13 ], and using multiple markers can reveal aspects, such as historical mitochondrial introgression, that may otherwise not be noticed [ 21 ]. Introgression is the exchange of genetic material between two species through hybridisation [ 22 ], and is particularly common in Larus gulls [ 23 , 24 ].…”