Integrative demographic inference in Iberian pond-breeding amphibians

Abstract

The main cause of the global amphibian crisis is the destruction of the habitats they need to forage, breed, hide, termorregulate or hibernate, although additional factors such as direct human exploitation, infectious diseases or the introduction of exotic invasive species are contributing to population eradications worldwide. Different policies are being implemented to counteract amphibian declines, mainly focused on protecting aquatic and terrestrial habitats, creating and adequating new breeding sites, reducing pathogen load in the wild or reinforcing population recruitment with captive breeding and release programs. However, the success and efficiency of these measures is compromised by wide gaps in the knowledge about the biology and demographic dynamics of most species. Recent advances in molecular and computational biology are complementing traditional field-based approaches, opening an unparalleled opportunity for molecular ecologists and evolutionary biologists to answer key questions about the biology, demography and natural history of many species. This dissertation takes advantage of molecular, theoretical and analytical developments in demographic research to explore some aspects of population dynamics and connectivity in four Iberian pond-breeding anurans: Epidalea calamita, Hyla molleri, Pelophylax perezi and Pelobates cultripes. An integrative framework based on 1) genetic data from 15-18 species-specific microsatellite markers, 2) an extensive sampling design including 13-19 populations per species across both slopes of a major mountain range in Central Spain and 3) a seven-year monitoring program in an amphibian assemblage based on capture-mark-recapture (CMR) techniques was implemented to infer some key demographic parameters including the effective/census size ratio and regional patterns of gene flow. First, I summarize the contributions and opportunities of molecular and individual-based CMR methods in demographic research and discuss how the integration of both approaches can be applied for conservation purposes (Chapter I). Chapters III and IV describe the three sets of specific microsatellite markers optimized for E. calamita, H. molleri and P. perezi, including a comprehensive summary on their polymorphism, genotyping error rates and information content, and assess their suitability for demographic research. Furthermore, I demonstrate that seven of the markers of the P. perezi set are useful for cross amplification and species assignment in the P. ridibundus x P. perezi hybridogenetic complex, each marker showing several private alleles for each of the parental species (Chapter III). Also, genetic diversity characterization in an extensive multi-population genotypic dataset revealed that FIS and tests of Hardy-Weinberg equilibrium and Linkage Disequilibrium (but not allelic richness and observed and expected heterozygosity) can be affected by the presence of full sibs in the sample (Chapter IV), which sheds light into this critical yet unresolved issue in population genetics and parentage analyses. A more comprehensive dataset obtained in a reference locality allowed developing a new method for calculating the minimum sample size required for estimating genetic diversity indexes with individual markers (Chapter IV). Chapters V and VI show that the application of previously-described molecular tools to adequate sampling designs, coupled with field-based data and CMR analyses can yield reliable estimates of the effective/census size ratio (Chapter V) and regional gene flow (Chapter VI). I demonstrate that anuran species with different life history traits show different local effective/census size ratios (Chapter V) and are differentially affected by the barrier effect exerted by a major mountain range (Chapter VI). Finally, I discuss the implications of these findings in the context of demographic and evolutionary research including possible applications for conservation purposes (Chapter VII).