Conservation genetics of threatened Mexican axolotls (Ambystoma) G. Parra-Olea 1 , K. R. Zamudio 2 , E. Recuero 3 , X. Aguilar-Miguel 4 , D. Huacuz 5 & L. Zambrano 1 1 Instituto de Biología, Universidad Nacional Autónoma de México, Distrito Federal, México 2 Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA 3 Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain 4 CIRB, Facultad de Ciencias, Universidad Autónoma del Estado de México, San Cayetano Toluca, Edo. de México, México 5 Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México Keywords paedomorphism; inbreeding; bottleneck; Trans-Mexican Volcanic Belt; endangered; Ambystoma; genetic diversity. Correspondence Gabriela Parra-Olea, Instituto de Biología, Universidad Nacional Autónoma de México. Distrito Federal, México, Tel: +52-55-5622- 9152; Fax: +52 55 5550 0164 Email: gparra@ibiologia.unam.mx Editor: David Reed Received 2 February 2011; accepted 15 July 2011 doi:10.1111/j.1469-1795.2011.00488.x Abstract The loss of genetic diversity in small or isolated populations can increase inbreed- ing, decrease fitness and adaptive potential and increase a species’ probability of extinction. In species with life histories that naturally result in small populations and/or low levels of gene flow, patterns of anthropogenically induced genetic erosion can be obscured by evolutionary history; yet these species may still be susceptible to genetic loss. We assess genetic diversity among populations of Ambystoma salamanders endemic to Mexico, including populations that are fac- ultatively or obligately paedomorphic, to test whether paedomorphic lineages have lower genetic diversity than metamorphic ones, and whether gene flow contributes to the maintenance of diversity in divergent forms with either life history. We also test the utility of our markers in assigning illegally harvested individuals to populations of origin. We found reduced genetic diversity in paedo- morphic compared with some, but not all, metamorphic populations. Populations of both forms showed genetic signatures of bottlenecks, underscoring that factors other than paedomorphosis contribute to historical reductions in population size. In general, Ambystoma populations have low interpopulation gene flow and admixture, but paedomorphic populations have higher within-population relat- edness than most metamorphic populations. We discuss historical and current landscape attributes that impact populations and their connectivity, the implica- tions of our findings for ongoing captive propagation programs and the prospects for continued genetic health of Ambystoma in México. Introduction The loss of genetic diversity in small or isolated populations is a concern for threatened species isolated by natural or anthropogenic barriers (Daniels, Triddy & Walters, 2000; Sherwin & Moritz, 2000). This genetic erosion will be exac- erbated in cases where isolated populations are small (Keller & Waller, 2002) as is often the case with threatened species in disturbed habitats (Andersen, Fog & Damgaard, 2004; Stow & Briscoe, 2005). Species with life history attributes that naturally result in small populations and/or limited dispersal often show the genetic signatures of low intrapopulation genetic diversity and limited interpopulation genetic exchange (Shaffer & Breden, 1989), which can confound signatures of anthropogenically induced genetic erosion. The Ambystoma species endemic to México are members of the widespread, polytypic, Ambystoma tigrinum complex (Shaffer, 1984a; Shaffer & McKnight, 1996; Recuero et al., 2010). Previous morphological (Shaffer, 1984b; Webb, 2004) and phylogenetic studies using allozymes (Shaffer, 1984a), mtDNA (Shaffer & McKnight, 1996; Recuero et al., 2010) and nuclear sequences (Weisrock et al., 2006) have examined species boundaries and divergences among regional groups of populations. Independent of the molecu- lar markers used, these studies corroborate that divergence of the Mexican forms, especially the narrow endemics, restricted to the Mexican Transvolcanic Belt (TVB), are very recent in origin. Lineages within the A. tigrinum complex are polymorphic for life history (Routman, 1993) and obligate paedomorphism has evolved multiple times in the endemic populations in México (Shaffer, 1984a; 1993). Based on this polymorphic life history trait, and their limited distribution in one or two lakes, some of these forms (but not all) have been named as independent species, but with no attention to relationships among taxa, reciprocal monophyly, and sometimes, the availability of diagnostic characters. Divergences among Mexican Ambystoma are generally shallow, resulting in low support for monophyletic Animal Conservation. Print ISSN 1367-9430 Animal Conservation 15 (2012) 61–72 © 2011 The Authors. Animal Conservation © 2011 The Zoological Society of London 61