RESEARCH ARTICLE Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi Fernando J. Mapelli • Matı ´as S. Mora • Patricia M. Mirol • Marcelo J. Kittlein Received: 25 November 2010 / Accepted: 12 September 2011 / Published online: 8 October 2011 Ó Springer Science+Business Media B.V. 2011 Abstract In order to devise adequate conservation and management strategies for endangered species, it is important to incorporate a reliable understanding of its spatial population structure, detecting the existence of demographic partitions throughout its geographical range and characterizing the distribution of its genetic diversity. Moreover, in species that occupy fragmented habitats it is essential to know how landscape characteristics may affect the genetic connectivity among populations. In this study we use eight microsatellite markers to analyze population structure and gene flow patterns in the complete geographic range of the endangered rodent Ctenomys porteousi. Also, we use landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connec- tivity among populations. In spite of geographical prox- imity of the sampling sites (8–27 km between the nearest sites) and the absence of marked barriers to individual movement, strong population structure and low values of gene flow were observed. Genetic differentiation among sampling sites was consistent with a simple model of iso- lation by distance, where peripheral areas showed higher population differentiation than those sites located in the central area of the species’ distribution. Landscape genetics analysis suggested that habitat fragmentation at regional level has affected the distribution of genetic variation among populations. The distance of sampling sites to areas of the landscape having higher habitat connectivity was the environmental factor most strongly related to population genetic structure. In general, our results indicate strong genetic structure in C. porteousi, even at a small spatial scale, and suggest that habitat fragmentation could increase the population differentiation. Keywords Population structure Á Landscape genetics Á Habitat fragmentation Á Ctenomys Introduction Natural populations occur in a landscape mosaic in which environmental features restrict or promote movements of individuals and genes affecting, as a consequence, migra- tion patterns among local populations and population structure (Taylor et al. 1993; Sork et al. 1999). When populations become fragmented in small demes and migration between them decreases or is eliminated, there is a consequent increase in inbreeding and loss of genetic diversity (Lande 1995; Frankham et al. 1999; Hurston et al. 2009). This scenario, together with environmental and demographic stochasticity, may have serious negative effects on the long term viability of local populations, and by extension, on the metapopulation as a whole (Keller et al. 1994; Lacy 1997; Bjilsma et al. 2000; Sherwin and Moritz 2000; Coulon et al. 2004). Studies of genetic dif- ferentiation in patchly landscapes can help to understand the effects of habitat fragmentation on population structure and to identify those landscape features that most affect dispersal and gene flow (Lampert et al. 2003; Funk et al. 2005). These studies can also help to define appropriate management units and to determine the extent to which F. J. Mapelli (&) Á M. S. Mora Á M. J. Kittlein Departamento de Biologı ´a, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to piso, 7600 Mar del Plata, Argentina e-mail: fmapelli@mdp.edu.ar P. M. Mirol Museo Argentino de Ciencias Naturales ‘‘Bernardino Rivadavia’’, Angel Gallardo 470, Buenos Aires, Argentina 123 Conserv Genet (2012) 13:165–181 DOI 10.1007/s10592-011-0273-2