Phylogeography of Invasive Rats in New Zealand

Abstract

Two species of invasive rats (Rattus norvegicus and R. rattus) arrived in New Zealand with Europeans in the mid to late eighteenth and nineteenth century respectively. They rapidly spread across the main islands of New Zealand and its offshore islands, displacing the historically introduced R. exulans. Today both species are widespread although the distribution of the subdominant R. norvegicus is patchy. Tissue samples were obtained from 425 R. rattus and 130 R. norvegicus across the New Zealand archipelago and neighboring islands. We sequenced a standard 545 base pair section of the mitochondrial D-loop in order to construct a modern phylogeography of the two species and to make inference on historical invasion pathways and spread across the country. We found limited diversity in R. norvegicus haplotypes, with two widespread haplotypes across New Zealand and its offshore islands most likely corresponding to two independent invasions, potentially with English and Chinese origins, respectively. In contrast we found widespread diversity in R. rattus haplotypes across New Zealand and its offshore islands, most likely corresponding to at least four independent invasions to the main North and South Islands, Great Barrier Island archipelago, and Stewart Island archipelago. The most common R. rattus haplogroup was found throughout New Zealand and many of its offshore islands, as well as neighboring islands in the Tasman Sea, and has been documented elsewhere across the Pacific, but with European origins. We also found both geographic partitioning and secondary invasions of haplotypes within the main North and South Island. In addition to distinct haplogroups differing by over three base pairs, which exhibit geographical partitioning suggestive of independent invasion events, for both species we also found instances of single base-pair differences within localities, elevating haplotype diversity. The geographical distribution of pelage color morphs also correlates with haplotype distribution, lending further support to the hypothesis and role of independent invasion events.

Commensal Rodents in 19th Century Australasia: Diversity, Invasion Routes and the China Connection

“…We designed the rat primers to sit within mitochondrial regions conserved between Rattus rattus and Rattus norvegicus. We expected to find that the majority of amplified D-loop variation in Sydney samples of both of these species to be similar to those recorded in a recent study of the mitochondrial genetic diversity of both species across New Zealand, because the diversities present in the two neighbouring countries are likely to be similar (Russell et al 2019). Similarly, we designed the mouse primers to sit within regions of the mitochondrial Dloop conserved between the three subspecies of Mus musculus (M. m. musculus, M. m. domesticus, and M. m. castaneus), amplifying the majority of D-loop variation recorded in recent studies of mice from New Zealand and Australia (King et al 2016;Veale et al 2018).…”

“…In the haplotype network (Figure 2) we have included the six R. norvegicus haplotypes labelled 1-6 identified in New Zealand by (Russell et al 2019). Haplotypes 1, 2 and 6, recorded only in New Zealand, are uncoloured, so as to facilitate later discussions of connections between the two countries.…”

“…All sequences were imported into Geneious (Kearse et al 2012), where we trimmed off the primer sequences, then aligned all modern and historical sequences for each species, along with the New Zealand mouse haplotypes from King et al (2016) and the rat haplotypes from Russell et al (2019). We then created haplotype networks for each species using the R packages ape (Paradis et al 2004;Paradis, Schliep 2019) and pegas (Paradis 2010).…”

Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies

“…This northern origin may explain the late start (thirteenth century AD) of global range expansion (Figure 1e); [ 27 ] first toward SEA and coastal ports, then into the Middle East and Europe via trade networks, and finally globally to western Africa, eastern North America, South America, and New Zealand. [ 28,29 ] Rats also expanded from the ancestral range eastward into China, Russia, and eventually to western North America. [ 28,30 ] Analyses from South Africa have identified multiple introductions, both from European [ 22 ] and an unknown source population.…”

Urban Rats in Wellington: Estimating Home Ranges, Population Densities and Detection Probabilities

“…Today the ship rat is the dominant species in New Zealand, with the Norway rat patchily distributed across the mainland and some offshore islands (Russell et al 2019). King et al (2011) found this was largely due to different foraging strategies as explained by the Marginal Value Theorem (MVT) (Charnov, 1976).…”