A perspective for resolving the systematics of Rattus, the vertebrates with the most influence on human welfare

Abstract

The murid rodent genus Rattus Fischer 1803 contains several species that are responsible for massive loss of crops and food, extinction of other species and the spread of zoonotic diseases to humans, as well as a laboratory species used to answer important questions in physiology, immunology, pharmacology, toxicology, nutrition, behaviour and learning. Despite the well-known significant impacts of Rattus, a definitive evolutionary based systematic framework for the genus is not yet available. The past 75 years have seen more dramatic changes in membership of Rattus than in almost any other genus of mammals. In fact, the Rattus genus has been a receptacle for any generalised Old World murine that lacked morphological specialisation and at one point, has included more than 560 species and/or subspecies, spread across Eurasia, Africa and the Australo-Papuan region. The dissolution of Rattus is ongoing as many of its constituent species and many genera of Rattini remain unsampled in any molecular study. To address this sampling limitation, we sequenced the mitochondrial cytochrome b (cytb) gene and examined phylogenetic relationships using both Bayesian and Maximum Likelihood algorithms for an expanded set of taxa within Rattus and among closely related genera. Here we place previously unsampled taxa in a phylogenetic context for the first time, including R. burrus, R. hoogerwerfi, R. lugens, and R. mindorensis within the Asian Rattus group, R. facetus within the Australo-Papuan Rattus radiation, and the undescribed ‘Bisa Rat’ described by Flannery as sister to the recently described genus Halmaheramys. We also present an exploratory foray into the wider topic of Rattus phylogenetics and propose that a reorganisation of the Rattus genus should require that it be a monophyletic group, include at least the type species R. norvegicus and R. rattus (plus their close allies); and exclude the Bandicota/Nesokia clade and other such specialised genera.

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

“…The integration of phylogeography and zooarchaeology offers immense promise to elucidate how urbanism and human communication and migration facilitated range expansions of commensal Rattus . Answering open questions regarding Rattus species delimitation, [ 3,5 ] biogeography, and repeating phylogeographic analyses with nuclear data will provide a strong foundation toward understanding both the evolution of commensalism and human‐commensal interactions. We see high value in taking a comparative approach between species to illuminate these processes.…”

“…Within the genus, the deepest divergence occurred between the Asian and Australo‐Papuan clades approximately 2.44 Mya, undergoing subsequent biogeographic structuring between New Guinea and Australia. [ 4 ] To date, mitochondrial phylogenies have included 26 or fewer species, [ 5 ] and comparisons between phylogenies with and without nuclear data identify mito‐nuclear discordance for some species. [ 4,6,7 ]…”

Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

“…The R. tiomanicus complex includes several insular forms ( R. burrus , R. simalurensis , R. adustus , R. palmarum , R. mindorensis , and R. lugens ), which are recognized as different species ( Musser and Carleton 2005 ). The molecular position has been evaluated for R. burrus , R. mindorensis , and R. lugens , which situates them within the Asian Rattus and close but outside R. tiomanicus ( Thomson et al 2018 ). Another species within the R. tiomanicus complex is Rattus blangorum .…”

“…Even after a profound morphological review of Sundaland Rattus , the origin and position of these lineages within Rattus remain unresolved ( Musser 1986 ). The evolutionary affinities at the molecular level between some of these linages and to other Rattus have been assessed with cytochrome b ( cyt b ) ( Aplin et al 2011 ; Thomson et al 2018 ), providing a comprehensive framework for molecular systematics of Rattus . However, they missed important taxa native to Sundaland (e.g., R. korinchi ), and they relied on cyt b alone, providing an incomplete evolutionary framework for Rattus native to Sundaland and their closest relatives in the Asian Rattus clade.…”

Late Quaternary Environmental and Human Impacts on the Mitochondrial DNA Diversity of Four Commensal Rodents in Myanmar

“…In Myanmar, commensal murine rodents are abundant and represented by the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus). Due to their large impacts on human welfare (Thomson et al 2018), it is necessary to elucidate the genetic structure and inferred demographics of commensal rodents in Myanmar.…”