Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome-wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next-generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander (Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this large data set (344 330 reads), we developed a pipeline that sorts PTS data by barcode and locus, identifies high-quality variable nucleotides and yields phased haplotype sequences for each individual at each locus. Our sequencing and bioinformatic strategy resulted in a genome-wide data set with relatively low levels of missing data and a wide range of nucleotide variation. structure analyses of these data in a genotypic format resulted in strongly supported assignments for the majority of individuals into nine geographically defined genetic clusters. Species tree analyses of the most variable loci using a multi-species coalescent model resulted in strong support for most branches in the species tree; however, analyses including more than 50 loci produced parameter sampling trends that indicated a lack of convergence on the posterior distribution. Overall, these results demonstrate the potential for amplicon-based PTS to rapidly generate large-scale data for population genetic and phylogenetic-based research.

The loss of genetic diversity in small or isolated populations can increase inbreeding, 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 facultatively 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 paedomorphic 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 relatedness than most metamorphic populations. We discuss historical and current landscape attributes that impact populations and their connectivity, the implications of our findings for ongoing captive propagation programs and the prospects for continued genetic health of Ambystoma in México. Animal Conservation. Print ISSN 1367-9430 Animal Conservation 15 (2012) 61-72

Se identifi caron 85 especies totales, de las cuales 24 especies son endémicas de México, 14 especies se encuentran en alguna categoría de riesgo de acuerdo con la NOM-059 (SEMARNAT, 2010) y 3especies en la lista roja de la UICN. Aun cuando la zona de estudio representa apenas el 0.42% de la superfi cie total del PNNT, la riqueza de vertebrados encontrada constituye el 11.37% de la riqueza total en el Estado de México, lo cual destaca la importancia de este espacio y una urgente necesidad de establecer estrategias de manejo que garanticen la conservación de las especies y su hábitat.Palabras clave: riqueza de especies, bosques reforestados, Área Natural Protegida, Estado de México, conservación y manejo.

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

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The North American tiger salamander species complex, including its flagship species the axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis and those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis). Such disparate life history strategies are assumed to cause populations to become reproductively isolated, but the degree to which they have actually shaped population- and species-level boundaries is poorly understood. Using a large multi-locus dataset from hundreds of samples across North America, we identified genetic clusters with clear signs of admixture across the geographic range of the tiger salamander complex. Population clusters often contain a mixture of paedomorphic and metamorphic taxa, and we conclude that geography has played a large role in driving lineage divergence relative to obligate paedomorphosis in this system. This conclusion is bolstered by model-based analyses demonstrating gene flow between metamorphic and paedomorphic populations. Even the axolotl, a paedomorphic species with an isolated native range, apparently has a history of gene flow with its neighboring populations. This fine-scale genetic perspective on life-history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. The axolotl is currently used as the vertebrate model system in regenerative biology, and our findings chart a course for more informed use of these and other tiger salamander species in experimental and field research, including conservation priorities.

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RESUMEN:Los anfibios están desapareciendo a nivel mundial. Varias especies se han perdido y miles más están en peligro de extinción. De las especies que están amenazadas, varias no se pueden proteger en su medio natural, por lo que es urgente realizar acciones de conservación ex situ que aseguren su preservación. Ambystoma granulosum y Ambystoma lermaense, son especies prioritarias para iniciar esta estrategia de conservación, ya que son especies endémicas de México y con un estatus de conservación preocupante. Ambas especies han sido poco estudiadas, por lo que en este estudio se investigaron, los aspectos reproductivos que son vitales para la conservación, logrando reproducir a la especie en condiciones de laboratorio de manera natural o espontánea, o por la estimulación hormonal con Gonadotropina Coriónica (hCG). Los resultados obtenidos nos indican que no existen diferencias significativas en la morfología de machos y hembras en ambas especies, excepto por el engrosamiento de la región cloacal en los machos. El ciclo reproductivo es anual y sincrónico en machos y hembras, con actividad máxima entre los meses de mayo a septiembre. Las puestas en parejas sin inducción hormonal fue variable con promedio de 664 ± 325 (DE) huevos y el porcentaje de fecundidad fue de 40 al 90%. En parejas de Ambystoma granulosum con inducción de hCG se obtuvieron nueve puestas variables entre 17 y 1182 huevos. En parejas de A. lermaense inducidos, se obtuvieron 16 puestas, las que variaron entre 110 y 1691 huevos. La fertilidad de los huevos inducidos fue muy variable analizándose posibles causas. Palabras clave: Ambystoma; Ambystoma granulosum; Ambystoma lermaense; reproducción; inducción hormonal con hCG. Recibido: 27/02/2007; aceptado: 11/05/2009.