The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.

Increasingly frequent “megafires” in North America's dry forests have prompted proposals to restore historical fire regimes and ecosystem resilience. Restoration efforts that reduce tree densities (eg via logging) could have collateral impacts on declining old‐forest species, but whether these risks outweigh the potential effects of large, severe fires remains uncertain. We demonstrate the effects of a 2014 California megafire on an iconic old‐forest species, the spotted owl (Strix occidentalis). The probability of owl site extirpation was seven times higher after the fire (0.88) than before the fire (0.12) at severely burned sites, contributing to the greatest annual population decline observed during our 23‐year study. The fire also rendered large areas of forest unsuitable for owl foraging one year post‐fire. Our study suggests that megafires pose a threat to old‐forest species, and we conclude that restoring historical fire regimes could benefit both old‐forest species and the dry forest ecosystems they inhabit in this era of climate change.

We identified six approaches to diagnosing causes of population declines and illustrate the use of the most general one ("multiple competing hypotheses") to determine which of three candidate limiting factors-food availability, nesting site availability, and nest predation-were responsible for the exceptionally poor reproduction of Marbled Murrelets ( Brachyramphus marmoratus) in central California. We predicted how six attributes of murrelet demography, behavior, and physiology should be affected by the candidate limiting factors and tested predictions with field data collected over 2 years. The average proportion of breeders, as estimated with radiotelemetry, was low (0.31) and varied significantly between years: 0.11 in 2000 and 0.50 in 2001. Murrelets spent significantly more time foraging in 2000 than in 2001, suggesting that low food availability limited breeding in 2000. In 2001, 50% of radio-marked murrelets nested and 67% of females were in breeding condition, suggesting that enough nest sites existed for much of the population to breed. However, rates of nest failure and nest predation were high (0.84 and 0.67-0.81, respectively) and few young were produced, even when a relatively high proportion of murrelets bred. Thus, we suggest that reproduction of Marbled Murrelets in central California is limited by food availability in some years and by nest predation in others, but apparently is not limited by availability of nesting sites. The multiple-competing-hypotheses approach provides a rigorous framework for identifying causes of population declines because it integrates multiple types of data sets and can incorporate elements of other commonly used approaches. Aplicación del Paradigma de la Población en Disminucioń: Diagnosis de las Causas de la Reproducción Deficiente de Brachyramphus marmoratus Resumen: Identificamos seis métodos utilizados para diagnosticar las causas de la disminucioń de poblaciones y damos un ejemplo del uso del más general ("hipótesis de competencia múltiple") para determinar cual de tres posibles factores limitantes (disponibilidad de alimento, disponibilidad de sitios de anidación y depredación de nidos) es responsable de la reproducción excepcionalmente deficiente de Brachyramphus marmoratus en California central. Predijimos el efecto de los factores limitantes sobre seis atributos de la demografía, comportamiento y fisiología de B. marmoratus, y probamos las predicciones con datos de campo recolectados a lo largo de 2 años. La proporción promedio de reproductores, estimada con radiotelemetría, fue baja (0.31) y varió significativamente entre años: 0.11 en 2000 y 0.50 en 2001. B. marmoratus forrajeó † Peery et al. Diagnosing Causes of Population Declines 1089 significativamente más tiempo en 2000 que en 2001, lo que sugiere que la baja disponibilidad de alimento limitó la reproducción en 2000. En 2001, 50% de los individuos radio-marcados anidó y 67% de las hembras estaban en condición reproductiva, lo que sugiere que existían suficientes sitios para nidos para la reproducción...

DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair "ZBJ" to results using the novel primer pair "ANML." To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre-and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization. K E Y W O R D SAMPtk, arthropod mock community, bat guano, dietary analysis, insectivore, next-generation sequencing *Indicates shared first authorship based on equal contributions.

Identifying source-sink dynamics is of fundamental importance for conservation but is often limited by an inability to determine how immigration and emigration influence population processes. We demonstrate two ways to assess the role of immigration on population processes without directly observing individuals dispersing from one population to another and apply these methods to a population of Marbled Murrelets (Brachyramphus marmoratus) in California (USA). In the first method, the rate of immigration (i) is estimated by subtracting local recruitment (recruitment from within the population due to reproduction) estimated with demographic data from total recruitment (f; recruitment from within the population plus recruitment from other populations) estimated using temporal symmetry mark-recapture models developed by R. Pradel. The second method compares population growth rates estimated with temporal symmetry models (lambdaTS) and/or population growth rates estimated from counts of individuals over multiple sampling periods (lambdaC) with growth estimates from a stage-structured projection matrix model (lambdaM). Both lambdaTS and lambdaC incorporate all demographic processes affecting population change (birth, death, immigration, and emigration), whereas matrix models are usually constructed without incorporating immigration. Thus, if lambdaTS and lambdaC are > or = 1 and lambdaM < 1, the population is sustained by immigration and is considered to be a sink. Using the first method, recruitment estimated with temporal symmetry models was high (f= 0.182, SE = 0.058), the mean adult birth rate, as estimated using the ratio of juveniles to > or = 1 year old individuals (observed during ship-based surveys) was low (bA = 0.039, SE = 0.014), and immigration was 0.160 (SE = 0.057). Using the second method, murrelet numbers in central California were stable (lambdaC = 1.058, SE = 0.047; lambdaTS = 1.064, SE = 0.033), but were projected to decline 9.5% annually in the absence of immigration (lambdaM = 0.905, SE = 0.053). Our results suggest that Marbled Murrelets in central California represent a sink population that is stable but would decline in the absence of immigration from larger populations to the north. However, the extent to which modeled immigration is due to permanent recruitment or temporarily dispersing individuals that simply mask population declines is uncertain.