Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in south Africa

Abstract

BackgroundSouth Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present.ResultsTo this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species.ConclusionsThis study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.

Cryptic genetic diversity in Rattus of the San Francisco Bay region, California

“…Bastos et al 2011, Chinen et al 2005 Lineage I (R. rattus), N = 20 Lineage II (R. tanezumi), N = 9 Musser and Carleton 2005;Pagès et al 2010;Robins et al 2007). In contrast, the results of the microsatellite analyses indicate that roof rats in the SF Bay Area comprise a single genetic population, with weak evidence of geographic subdivision but no indication of subdivision by the mtDNA Lineages.…”

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

“…To further illustrate this point, mice with both DOM and CAS mtDNA haplotypes have been captured in Japanese international ports (Tsuda et al, 2007) and Nunome et al (2010a) provided robust evidence from their nuclear haplotype analysis of genetic introgression by DOM components of Japanese house mice. The extent to which genetic introgression may now be shaping the future evolution of the house mouse is an interesting topic-one that has bearing on other commensal mammals, including the black rat Rattus rattus which also displays comparable signals of former geographic sub-division and recent intermingling as a consequence of commensalism and human-assisted dispersal (Chinen et al, 2005;Aplin et al, 2011;Bastos et al, 2011;Lack et al, 2012).…”

Diversity and endemism of Murinae rodents in Thai limestone karsts

“…The genus Rattus and in particular the Rattus rattus complex represents one of the best examples of this minimal external morphological divergence among Rattini species that evolved rapidly and recently and that are differentiated only by subtle morphological variations . DNA-based approaches have recently proved to be useful tools to clarify the complex taxonomy of Rattini and especially of the Rattus genus (Robins et al, 2007;Pages et al, 2010;Aplin et al, 2011;Bastos et al, 2011) and helped to elucidate the specific status of several Rattus cryptic species such as Rattus losea and Rattus sakeratensis (formerly treated as a synonym of R. losea) or Rattus rattus and Rattus satarae (formerly treated as a subspecies of R. rattus) (Pages et al, 2011). Discovery and description of cryptic species is particularly important for conservation and natural resources management as design of conservation strategies mainly relies on estimates of species richness and endemism (Bickford et al, 2007).…”