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Time and financial constraints often force conservationists to make ad hoc management decisions without sufficient knowledge to predict their effects. In particular, the effects of management on reproduction and survival are rarely evaluated and habitat dynamics are rarely taken into account. We evaluated the effects of three different forms of habitat alteration on the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador during the phases of population increase and stabilization. More specifically, we monitored the effect of a natural experiment with three approaches (clearing, grazing and burning) to preserve the semi-open habitat of this species on the reproductive success of 220 breeding events over seven years and on the survival of 73 adults over three consecutive years. Habitat alteration had contrasting effects on reproduction and survival. All approaches increased the number of fledged chicks per breeding event while the population stabilized, but not while it increased. However, vegetation burning reduced survival probability of adult individuals. In addition, survival was strongly correlated to the presence of water in the territories. Overall, we revealed that the negative effects of vegetation burning on survival overrode the positive effects on reproduction, and could—if implemented at a larger scale—destroy the conservation aim of increasing the population size. Importantly, we show that the effectiveness of management differs depending on the actual population trend. Our study therefore shows that the a posteriori evaluation of ad hoc vegetation control can constitute an integral part of adaptive management and thereby also of long-term conservation planning of endangered species.

Density-dependent processes are fundamental mechanisms for the regulation of populations. Ecological theories differ in their predictions on whether increasing population density leads to individual adjustments of survival and reproductive output or to dominance and monopolization of resources. Here, we use a natural experiment to examine which factors limit population growth in the only remaining population of the endangered pale-headed brush finch (Atlapetes pallidiceps). For three distinct phases (a phase of population suppression, 2001–2002; expansion due to conservation management, 2003–2008; and equilibrium phase, 2009–2014), we estimated demographic parameters with an integrated population model using population size, the proportion of successfully breeding pairs and their productivity, territory size, and mark-recapture data of adult birds. A low proportion of successful breeders due to brood parasitism (0.42, 95% credible interval 0.26–0.59) limited population growth before 2003; subsequent culling of the brood parasite resulted in a two-fold increase of the proportion of successful breeders during the ‘expansion phase’. When the population approached the carrying capacity of its habitat, territory size declined by more than 50% and fecundity declined from 1.9 (1.54–2.27) to 1.3 (1.12–1.53) chicks per breeding pair, but the proportion of successful breeders remained constant (expansion phase: 0.85; 0.76–0.93; equilibrium phase: 0.86; 0.79–0.92). This study demonstrates that limiting resources can lead to individual adjustments instead of despotic behavior, and the individual reduction of reproductive output at high population densities is consistent with the slow life-history of many tropical species.

Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll-like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale-headed Brushfinch with two co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species.