Genetic analyses on noninvasively collected samples have revolutionized how populations are monitored. Most noninvasive monitoring studies have used hair or scat for individual identification of elusive mammals, but here we utilize naturally shed feathers. The Eastern imperial eagle (EIE) is a species of conservation concern throughout Central Asia and, like most raptors, EIEs are inherently challenging to study because adults are difficult to capture and band using conventional techniques. Over 6 years, we noninvasively collected hundreds of adult feathers and directly sampled EIE chicks at a national nature reserve in Kazakhstan. All samples were genetically sexed and genotyped at a suite of microsatellite loci. Genetically profiled adult feathers identified and monitored the presence of individual eagles over time, enabling us to address a variety of issues related to the biology, demography, and conservation of EIEs. Specifically, we characterized (i) the genetic mating system, (ii) relatedness among mated pairs, (iii) chick sex ratios, and (iv) annual turnover in an adult breeding population. We show that EIEs are genetically monogamous and furthermore, there is no apparent relatedness-based system of mate choice (e.g. inbreeding avoidance). Results indicate that annual adult EIE survivorship (84%) is lower than expected for a long-lived raptor, but initial analyses suggest the current reproductive rate at our study site is sufficient to maintain a stable breeding population. The pristine habitat at our study site supports an EIE population that is probably the most demographically robust in the world; thus, our results caution that populations in marginal habitats may not be self-sustaining.

The demographic consequences of within-population variability in predator foraging are not well understood. We assessed the relationship between the degree of diet specialization and two demographic parameters, population density and reproductive output, within a single population of Imperial Eagles Aquila heliaca at a nature reserve in north-central Kazakhstan. Nearest-neighbour distances between eagle nests throughout the reserve, and thus population density, were correlated with the degree to which diets were specialized. Diet diversity showed an extensive regional variability that was linked to prey distributions, but withinyear analyses of reproductive output did not show similar linkages. However, multi-year analyses of breeding performance showed inter-regional differences in nesting success that were paralleled, and probably driven by, similar trends in diet diversity. In contrast, brood size at fledging was not linked to diet diversity and was more probably driven by reservewide influences such as weather. Finally, the decision to initiate breeding was associated neither with diet diversity nor with environmental variability. Our results indicate that the degree of dietary specialization is linked to the demographics of Imperial Eagle populations. For these and other raptor populations, it is possible that management could be used separately to increase or decrease nesting success, brood size at fledging, and the likelihood that a pair will initiate breeding.

Estimating population size is central to species-oriented conservation and management. However, in spite of recent development in monitoring protocols, there are gaps in our ability to accurately and quickly estimate numbers of individuals present, especially for the cryptic and often non-breeding components of structured vertebrate populations. Yet knowing the size and growth trajectory of all stage classes of a population is critical for species conservation. Here we use data from 2 years of non-invasive genetic sample collection from the cryptic, nonbreeding component of an endangered bird of prey population to evaluate the impact of variability in population estimates on demographic models that underpin conservation efforts. A single non-invasive sample collection in 2003 conclusively identified 47 individual non-breeding imperial eagles, 2.8 times more than were visually counted. In 2004, our comprehensive genetic and observational analyses determined that 414 imperial eagles (n = 308 non-breeders+68 territory holders+38 chicks) were present. This estimate was 326% larger than the 127 birds visually observed (n = 21 non-breeders+68 territory holders+38 chicks) and 265% larger than the population size predicted by demographic models with the same number of breeders (n= 156 AE 7.2; AE SE). Our study builds on a body of work that demonstrates that conventional visual estimation of cryptic components of structured populations may not always be effective. Furthermore, we show that reliance on those estimates can result in inaccuracies in the demographic models that are often the foundation for subsequent conservation action.

Roughly one-third of all eagle species are considered to be threatened or endangered, but the ecology of most eagles remains poorly understood. While the pronounced territoriality of breeding adults facilitates behavioral studies, the demography of non-breeding individuals (pre-adults and non-territorial floaters) is almost completely unknown. Traditionally, limited data on preadult and floater movement come from wing-tagging and/ or telemetry studies. As an alternative to these methods we used genetic analyses of non-invasively collected feathers to investigate the population biology of non-breeding eastern imperial eagles (Aquila heliaca) in Kazakhstan. Microsatellite profiles of shed feathers indicate that eastern imperial eagles roost communally with other raptors. Furthermore, roosts are large and dynamic: 287 non-breeding eastern imperial eagles were detected in our sample, and a mark-recapture analysis estimated the total number to be 308 ± 8. The natal origins of these individuals were investigated by comparing their microsatellite profiles to those available for >90% of the eastern imperial eagle chicks hatched at the study site over the six previous breeding seasons. Only 4% of the individuals genetically matched a chick, suggesting that the reserve may serve as a critical refugium for pre-adults and itinerant floaters. Feathers have long been recognized as a suitable source of DNA, but few studies have used wide-scale, non-invasive collections of feathers (>1,000 samples) to investigate fundamental aspects of avian biology. Our research demonstrates that non-invasive genetic analyses of feathers can be used to evaluate population size, natal philopatry, and local movements of birds that are difficult to study using traditional means.

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