Applications of Molecular Biology to Managing Invasive Rodents on New Zealand Islands

Abstract

Three species of invasive rodents (Rattus norvegicus, R. rattus and Mus musculus) have accompanied humans worldwide as commensals and can be found virtually throughout the globe, with few exceptions. This global conquest and their invasion success is not solely based on virtue of being highly adaptive species: their ability to survive in a broad range of climates and their capability of preying, foraging and digesting a wide spectrum of food. Their vast distribution is also tightly connected with human dispersal. Rats and mice have accompanied humans on each voyage and have subsequently reached the remotest places. Such human facilitated transfer out of their native range, into a new environment, combined with high reproduction rates, has had far reaching effects on native native species after arrival. Especially on islands, such biological invasions are particularly devastating for the ecosystem. The ultimate goal in pest management is to contain and reverse the devastating consequences of invasive species. Most notably, nearshore islands are facing particular challenges, as reinvasion dispersal is important where pests self-colonise islands unaided by humans. The population dynamics and genetic structure of invasive species are often additionally elucidated to ensure the success of pest management goals. Typically this is done in a two stage process, both before and after eradication to evaluate success, leading to stronger conservation management. First, the thesis focuses on two different case studies demonstrating the application of modern population genetics tools to invasive rodent management. The first study looks at a ship rat (Rattus rattus) invasion on a small nearshore island in the Goat Island marine reserve. The metapopulation dynamics and pest control success on the island were evaluated using samples stemming from a multi-year control program for seabird conservation. Moderate genetic differentiation between the two populations was found despite their close proximity and it was demonstrated that rats were neither being removed faster than they bred nor was reinvasion able to be managed close to zero. The second study concentrates on house mice (Mus musculus) invasions on several nearshore islands in the upper South Island. Regional invasion pathways were determined in order to establish the potential source population and to assess the magnitude of biosecurity breach. Mice found on the reinvaded islands had genetic profiles consistent with the adjacent mainland, which confirmed the success of eradication, but failure of biosecurity procedures. Both projects utilized microsatellite loci and the results demonstrate that the application of molecular genetics strongly enhances pest management decisions. This highlights the need for better biosecurity measures to reduce the likelihood of invasion of nearshore islands by either swimming or hitchhiking. Understanding the genetic makeup of these invasive species could be the next step-change towards better management. In consideration of New Zealand’s ambitious intention to eradicate the most damaging mammalian predators by 2050, a draft genome assembly of Rattus rattus, the most widespread rat species in NZ, could lead to the development of novel genetic tools and certainly be a valuable resource for future genetic studies of this cryptic species. The next study in this thesis summarises the work completed towards a first draft assembly of a R. rattus genome, which as to this date has not been published. This is striking as the species is responsible for the spread of zoonotic disease, local extinctions and annually causes a substantial amount of financial damage, particularly on islands. The foundation for the genome sequence was laid by testing different tissue samples from wild ship rats to extract high quality DNA, whole genome sequencing using Illumina HiSeq sequencing and draft assembly of a single individual. Two different assembly methods were compared and a workflow has been suggested for further improvement of the draft assembly in collaboration with an international consortium. Although established genetic methods provide reliable results, novel molecular tools, like developing a single nucleotide polymorphism (SNP) panel, are the next logical step, given they are very cost-effective and quick to run, once established. SNPs offer a variety of advantages over microsatellite markers in genetic studies: they are highly abundant throughout the genome, allow higher throughput and are less error prone to amplification and scoring mistakes. A set of high quality SNPs, based on whole genome sequencing of R. rattus in reference to the R. norvegicus genome, has been identified. These SNPs were further tested on a number of individuals from a broad geographical range covering New Zealand and neighbouring countries using MassARRAY genotyping. Utilization of this SNP panel for genetic evaluation and implementation in future conservation management projects will provide another level of information, increase accuracy of population structure and invasion histories, while allowing higher throughput with lower costs.